diff --git a/uk/ac/sanger/artemis/components/EntryGroupInfoDisplay.java b/uk/ac/sanger/artemis/components/EntryGroupInfoDisplay.java
index 960ab6112e0ddea70a4ef7454fc5f3ed28787b20..5faa63d61c2faf6febea8e4f5f4b1eb9ab07f68d 100644
--- a/uk/ac/sanger/artemis/components/EntryGroupInfoDisplay.java
+++ b/uk/ac/sanger/artemis/components/EntryGroupInfoDisplay.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EntryGroupInfoDisplay.java,v 1.1 2004-06-09 09:46:30 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EntryGroupInfoDisplay.java,v 1.2 2004-12-14 15:53:11 tjc Exp $
**/
package uk.ac.sanger.artemis.components;
@@ -47,21 +47,28 @@ import javax.swing.JFrame;
* show the sequence length, GC content and a summary of the active entries.
*
* @author Kim Rutherford
- * @version $Id: EntryGroupInfoDisplay.java,v 1.1 2004-06-09 09:46:30 tjc Exp $
+ * @version $Id: EntryGroupInfoDisplay.java,v 1.2 2004-12-14 15:53:11 tjc Exp $
**/
public class EntryGroupInfoDisplay
implements FeatureChangeListener, EntryChangeListener,
- EntryGroupChangeListener, SequenceChangeListener {
+ EntryGroupChangeListener, SequenceChangeListener
+{
+ /**
+ * Summarize both strands.
+ **/
+ final static public int BOTH = 3;
+
/**
* Create a new EntryGroupInfoDisplay object to summarize all features on
* both strands of the given EntryGroup.
* @param parent_frame The reference of the parent JFrame.
* @param entry_group The EntryGroup to view.
**/
- public EntryGroupInfoDisplay (final JFrame parent_frame,
- final EntryGroup entry_group) {
- this (parent_frame, entry_group, BOTH);
+ public EntryGroupInfoDisplay(final JFrame parent_frame,
+ final EntryGroup entry_group)
+ {
+ this(parent_frame, entry_group, BOTH);
}
/**
@@ -73,60 +80,71 @@ public class EntryGroupInfoDisplay
* summarize all features on both strands. FORWARD means summarize
* forward strand only. REVERSE means summarize reverse strand only.
**/
- public EntryGroupInfoDisplay (final JFrame parent_frame,
- EntryGroup entry_group,
- final int strand_flag) {
+ public EntryGroupInfoDisplay(final JFrame parent_frame,
+ EntryGroup entry_group,
+ final int strand_flag)
+ {
this.strand_flag = strand_flag;
this.parent_frame = parent_frame;
this.entry_group = entry_group;
- if (strand_flag == FORWARD) {
+ if(strand_flag == Bases.FORWARD)
+ {
final FeaturePredicate forward_feature_predicate =
- new FeaturePredicate () {
- public boolean testPredicate (final Feature test_feature) {
- return test_feature.isForwardFeature ();
- }
- };
+ new FeaturePredicate()
+ {
+ public boolean testPredicate(final Feature test_feature)
+ {
+ return test_feature.isForwardFeature();
+ }
+ };
final FilteredEntryGroup filtered_entry_group =
- new FilteredEntryGroup (entry_group, forward_feature_predicate,
- "forward strand features");
+ new FilteredEntryGroup(entry_group, forward_feature_predicate,
+ "forward strand features");
entry_group = filtered_entry_group;
- } else {
- if (strand_flag == REVERSE) {
+ }
+ else
+ {
+ if(strand_flag == Bases.REVERSE)
+ {
final FeaturePredicate reverse_feature_predicate =
- new FeaturePredicate () {
- public boolean testPredicate (final Feature test_feature) {
- return !test_feature.isForwardFeature ();
- }
- };
+ new FeaturePredicate()
+ {
+ public boolean testPredicate(final Feature test_feature)
+ {
+ return !test_feature.isForwardFeature();
+ }
+ };
final FilteredEntryGroup filtered_entry_group =
- new FilteredEntryGroup (entry_group, reverse_feature_predicate,
- "reverse strand features");
+ new FilteredEntryGroup(entry_group, reverse_feature_predicate,
+ "reverse strand features");
entry_group = filtered_entry_group;
- } else {
- if (strand_flag != BOTH) {
- throw new Error ("internal error - illegal argument");
- }
+ }
+ else
+ {
+ if(strand_flag != BOTH)
+ throw new Error("internal error - illegal argument");
}
}
- file_viewer = new FileViewer (getFrameName ());
+ file_viewer = new FileViewer(getFrameName());
+ updateView();
- updateView ();
+ entry_group.addEntryChangeListener(this);
+ entry_group.addFeatureChangeListener(this);
+ entry_group.addEntryGroupChangeListener(this);
+ entry_group.getBases().addSequenceChangeListener(this,
+ Bases.MAX_PRIORITY);
- entry_group.addEntryChangeListener (this);
- entry_group.addFeatureChangeListener (this);
- entry_group.addEntryGroupChangeListener (this);
- entry_group.getBases ().addSequenceChangeListener (this,
- Bases.MAX_PRIORITY);
-
- file_viewer.addWindowListener (new WindowAdapter () {
- public void windowClosed (WindowEvent event) {
- stopListening ();
+ file_viewer.addWindowListener(new WindowAdapter()
+ {
+ public void windowClosed(WindowEvent event)
+ {
+ stopListening();
}
});
}
@@ -134,64 +152,53 @@ public class EntryGroupInfoDisplay
/**
* Return the String that should be used for the title of the Overview Frame
**/
- private String getFrameName () {
- if (entry_group instanceof FilteredEntryGroup) {
+ private String getFrameName()
+ {
+ if(entry_group instanceof FilteredEntryGroup)
+ {
final FilteredEntryGroup filtered_entry_group =
- (FilteredEntryGroup) entry_group;
+ (FilteredEntryGroup)entry_group;
- final String filter_name = filtered_entry_group.getFilterName ();
+ final String filter_name = filtered_entry_group.getFilterName();
- if (filter_name == null) {
- return "Artemis overview of: " + parent_frame.getTitle ();
- } else {
- return "Artemis overview of: " + parent_frame.getTitle () +
+ if(filter_name == null)
+ return "Artemis overview of: " + parent_frame.getTitle();
+ else
+ return "Artemis overview of: " + parent_frame.getTitle() +
" (" + filter_name + ")";
- }
- } else {
- final StringBuffer buffer = new StringBuffer ("Artemis Overview");
-
- if (entry_group.size () > 0) {
-
- buffer.append (" of:");
-
- for (int i = 0 ; i < entry_group.size () ; ++i) {
- final Entry this_entry = entry_group.elementAt (i);
-
- if (this_entry.getName () == null) {
- buffer.append (" [no name]");
- } else {
- buffer.append (" " + this_entry.getName ());
- }
+ }
+ else
+ {
+ final StringBuffer buffer = new StringBuffer("Artemis Overview");
+
+ if(entry_group.size() > 0)
+ {
+ buffer.append(" of:");
+
+ for(int i = 0 ; i < entry_group.size() ; ++i)
+ {
+ final Entry this_entry = entry_group.elementAt(i);
+
+ if(this_entry.getName() == null)
+ buffer.append(" [no name]");
+ else
+ buffer.append(" " + this_entry.getName());
}
}
- return buffer.toString ();
+ return buffer.toString();
}
}
- /**
- * Use the forward strand when summarizing.
- **/
- final static public int FORWARD = Bases.FORWARD;
-
- /**
- * Use the reverse strand when summarizing.
- **/
- final static public int REVERSE = Bases.REVERSE;
-
- /**
- * Summarize both strands.
- **/
- final static public int BOTH = 3;
-
/**
* Remove this object as a selection change listener.
**/
- private void stopListening () {
- entry_group.removeEntryChangeListener (this);
- entry_group.removeEntryGroupChangeListener (this);
- entry_group.removeFeatureChangeListener (this);
- entry_group.getBases ().removeSequenceChangeListener (this);
+ private void stopListening()
+ {
+ entry_group.removeEntryChangeListener(this);
+ entry_group.removeEntryGroupChangeListener(this);
+ entry_group.removeFeatureChangeListener(this);
+ entry_group.getBases().removeSequenceChangeListener(this);
}
/**
@@ -199,8 +206,9 @@ public class EntryGroupInfoDisplay
* FeatureChange events so that we can update the display if qualifiers
* change.
**/
- public void featureChanged (final FeatureChangeEvent event) {
- updateView ();
+ public void featureChanged(final FeatureChangeEvent event)
+ {
+ updateView();
}
/**
@@ -208,13 +216,15 @@ public class EntryGroupInfoDisplay
* EntryGroupChange events so that we can update the display if entries
* are added, deleted, activated or deactivated.
**/
- public void entryGroupChanged (final EntryGroupChangeEvent event) {
- if (event.getType () == EntryGroupChangeEvent.DONE_GONE) {
- stopListening ();
- file_viewer.dispose ();
- } else {
- updateView ();
+ public void entryGroupChanged(final EntryGroupChangeEvent event)
+ {
+ if(event.getType() == EntryGroupChangeEvent.DONE_GONE)
+ {
+ stopListening();
+ file_viewer.dispose();
}
+ else
+ updateView();
}
/**
@@ -222,8 +232,9 @@ public class EntryGroupInfoDisplay
* EntryChange events so that we can update the display if features are
* added or deleted.
**/
- public void entryChanged (final EntryChangeEvent event) {
- updateView ();
+ public void entryChanged(final EntryChangeEvent event)
+ {
+ updateView();
}
/**
@@ -231,287 +242,299 @@ public class EntryGroupInfoDisplay
* SequenceChange events so that we can update the display if the sequence
* changes.
**/
- public void sequenceChanged (final SequenceChangeEvent event) {
- updateView ();
+ public void sequenceChanged(final SequenceChangeEvent event)
+ {
+ updateView();
}
/**
* Update the FileViewer component to reflect the current state of the
* EntryGroup.
**/
- private void updateView () {
- final String frame_name = getFrameName ();
-
- file_viewer.setTitle (frame_name);
+ private void updateView()
+ {
+ final String frame_name = getFrameName();
+ file_viewer.setTitle(frame_name);
- final StringBuffer buffer = new StringBuffer ();
-
- buffer.append (frame_name + "\n\n");
+ final StringBuffer buffer = new StringBuffer();
- buffer.append ("Number of bases: " +
- entry_group.getSequenceLength () + "\n");
- buffer.append ("Number of features in the active entries: " +
- entry_group.getAllFeaturesCount () + "\n\n");
+ buffer.append(frame_name + "\n\n");
+ buffer.append("Number of bases: " +
+ entry_group.getSequenceLength() + "\n");
+ buffer.append("Number of features in the active entries: " +
+ entry_group.getAllFeaturesCount() + "\n\n");
- final Bases entry_group_bases = entry_group.getBases ();
+ final Bases entry_group_bases = entry_group.getBases();
// cds_count - gene_count = pseudo gene count
int gene_count = 0;
- int cds_count = 0;
+ int cds_count = 0;
int spliced_gene_count = 0;
int spliced_gene_bases_count = 0;
- StringBuffer gene_bases_buffer = new StringBuffer ();
+
+ StringBuffer gene_bases_buffer = new StringBuffer();
int gene_bases_count_with_introns = 0;
int cds_bases_count = 0;
- int exon_count = 0;
- int intron_count = 0;
- int partial_count = 0;
+ int exon_count = 0;
+ int intron_count = 0;
+ int partial_count = 0;
- final Hashtable table = new Hashtable ();
+ final Hashtable table = new Hashtable();
+ final FeatureEnumeration feature_enumerator = entry_group.features();
- final FeatureEnumeration feature_enumerator = entry_group.features ();
+ while(feature_enumerator.hasMoreFeatures())
+ {
+ final Feature this_feature = feature_enumerator.nextFeature();
- while (feature_enumerator.hasMoreFeatures ()) {
- final Feature this_feature = feature_enumerator.nextFeature ();
+ final Key key = this_feature.getKey();
+ final String key_string = key.toString();
- final Key key = this_feature.getKey ();
- final String key_string = key.toString ();
+ final Location location = this_feature.getLocation();
+ final RangeVector ranges = location.getRanges();
- final Location location = this_feature.getLocation ();
-
- final RangeVector ranges = location.getRanges ();
-
- for (int i = 0 ; i < ranges.size () ; ++i) {
- if (ranges.elementAt (i) instanceof FuzzyRange) {
+ for(int i = 0; i < ranges.size(); ++i)
+ if(ranges.elementAt(i) instanceof FuzzyRange)
++partial_count;
- }
- }
- try {
- String colour = this_feature.getValueOfQualifier ("colour");
+ try
+ {
+ String colour = this_feature.getValueOfQualifier("colour");
- if (colour == null || colour.length () == 0) {
+ if(colour == null || colour.length() == 0)
colour = "no colour";
- }
-
- if (table.containsKey (key_string)) {
- final Hashtable colour_table = (Hashtable) table.get (key_string);
- final Integer colour_value = (Integer) colour_table.get (colour);
-
- if (colour_value == null) {
- colour_table.put (colour, new Integer (1));
- } else {
- final int old_value = ((Integer) colour_value).intValue ();
-
- colour_table.put (colour, new Integer (old_value + 1));
+ if(table.containsKey(key_string))
+ {
+ final Hashtable colour_table = (Hashtable)table.get(key_string);
+ final Integer colour_value = (Integer)colour_table.get(colour);
+
+ if(colour_value == null)
+ colour_table.put(colour, new Integer(1));
+ else
+ {
+ final int old_value = ((Integer)colour_value).intValue();
+ colour_table.put(colour, new Integer(old_value + 1));
}
- } else {
- final Hashtable colour_table = new Hashtable ();
- colour_table.put (colour, new Integer (1));
- table.put (key_string, colour_table);
+ }
+ else
+ {
+ final Hashtable colour_table = new Hashtable();
+ colour_table.put(colour, new Integer(1));
+ table.put(key_string, colour_table);
}
- } catch (InvalidRelationException e) {
- throw new Error ("internal error - unexpected exception: " + e);
+ }
+ catch(InvalidRelationException e)
+ {
+ throw new Error("internal error - unexpected exception: " + e);
}
- if (this_feature.isCDS ()) {
+ if(this_feature.isCDS())
+ {
cds_count++;
-
- cds_bases_count += this_feature.getBaseCount ();
+ cds_bases_count += this_feature.getBaseCount();
final Qualifier pseudo_qualifier;
- try {
- pseudo_qualifier = this_feature.getQualifierByName ("pseudo");
- } catch (InvalidRelationException e) {
- throw new Error ("internal error - unexpected exception: " + e);
+ try
+ {
+ pseudo_qualifier = this_feature.getQualifierByName("pseudo");
+ }
+ catch(InvalidRelationException e)
+ {
+ throw new Error("internal error - unexpected exception: " + e);
}
- if (pseudo_qualifier == null) {
+ if(pseudo_qualifier == null)
+ {
++gene_count;
- final FeatureSegmentVector segments = this_feature.getSegments ();
+ final FeatureSegmentVector segments = this_feature.getSegments();
- if (segments.size () > 1) {
+ if(segments.size() > 1)
+ {
++spliced_gene_count;
- spliced_gene_bases_count += this_feature.getBaseCount ();
- intron_count += segments.size () - 1;
+ spliced_gene_bases_count += this_feature.getBaseCount();
+ intron_count += segments.size() - 1;
}
- exon_count += segments.size ();
+ exon_count += segments.size();
- gene_bases_buffer.append (this_feature.getBases ());
+ gene_bases_buffer.append(this_feature.getBases());
- gene_bases_count_with_introns +=
- this_feature.getRawLastBase () -
- this_feature.getRawFirstBase () + 1;
+ gene_bases_count_with_introns += this_feature.getRawLastBase() -
+ this_feature.getRawFirstBase() + 1;
}
}
}
- final String gene_bases = gene_bases_buffer.toString ();
- final int gene_bases_count = gene_bases.length ();
+ final String gene_bases = gene_bases_buffer.toString();
+ final int gene_bases_count = gene_bases.length();
final int pseudo_gene_count = cds_count - gene_count;
final int pseudo_gene_bases_count = cds_bases_count - gene_bases_count;
- if (cds_count > 0) {
- if (gene_count > 0) {
- buffer.append ("Genes (CDS features without a /pseudo qualifier):\n");
+ if(cds_count > 0)
+ {
+ if(gene_count > 0)
+ {
+ buffer.append("Genes (CDS features without a /pseudo qualifier):\n");
final int non_spliced_gene_count = gene_count - spliced_gene_count;
final int non_spliced_gene_bases_count =
gene_bases_count - spliced_gene_bases_count;
- if (spliced_gene_count > 0) {
- buffer.append (" spliced:\n");
- buffer.append (" count: " + spliced_gene_count + "\n");
- buffer.append (" bases: " + spliced_gene_bases_count + "\n");
- buffer.append (" introns: " + intron_count + "\n");
+ if(spliced_gene_count > 0)
+ {
+ buffer.append(" spliced:\n");
+ buffer.append(" count: " + spliced_gene_count + "\n");
+ buffer.append(" bases: " + spliced_gene_bases_count + "\n");
+ buffer.append(" introns: " + intron_count + "\n");
}
- if (non_spliced_gene_count > 0) {
- buffer.append (" non-spliced:\n");
- buffer.append (" count: " + non_spliced_gene_count + "\n");
- buffer.append (" bases: " + non_spliced_gene_bases_count +
- "\n");
+ if(non_spliced_gene_count > 0)
+ {
+ buffer.append(" non-spliced:\n");
+ buffer.append(" count: " + non_spliced_gene_count + "\n");
+ buffer.append(" bases: " + non_spliced_gene_bases_count +
+ "\n");
}
- buffer.append (" all:\n");
- buffer.append (" count: " + gene_count + "\n");
- buffer.append (" partials: " + partial_count + "\n");
- if (exon_count == gene_count) {
- buffer.append (" bases: "
- + gene_bases_count + "\n");
- } else {
- buffer.append (" bases (excluding introns): "
- + gene_bases_count + "\n");
- buffer.append (" bases (including introns): "
- + gene_bases_count_with_introns + "\n");
- buffer.append (" exons: " + exon_count + "\n");
- buffer.append (" average exon length: " +
- 10L * gene_bases_count / exon_count / 10.0 + "\n");
- buffer.append (" average intron length: " +
- 10L * (gene_bases_count_with_introns -
- gene_bases_count) /
- (exon_count - gene_count) / 10.0 + "\n");
- buffer.append (" average number of exons per gene: " +
- 100L * exon_count / gene_count / 100.00 + "\n");
+ buffer.append(" all:\n");
+ buffer.append(" count: " + gene_count + "\n");
+ buffer.append(" partials: " + partial_count + "\n");
+ if(exon_count == gene_count)
+ {
+ buffer.append(" bases: "
+ + gene_bases_count + "\n");
+ }
+ else
+ {
+ buffer.append(" bases(excluding introns): "
+ + gene_bases_count + "\n");
+ buffer.append(" bases(including introns): "
+ + gene_bases_count_with_introns + "\n");
+ buffer.append(" exons: " + exon_count + "\n");
+ buffer.append(" average exon length: " +
+ 10L * gene_bases_count / exon_count / 10.0 + "\n");
+ buffer.append(" average intron length: " +
+ 10L * (gene_bases_count_with_introns -
+ gene_bases_count) /
+ (exon_count - gene_count) / 10.0 + "\n");
+ buffer.append(" average number of exons per gene: " +
+ 100L * exon_count / gene_count / 100.00 + "\n");
}
- buffer.append (" density: " +
- 1000000L * gene_count /
- entry_group.getSequenceLength () / 1000.0 +
- " genes per kb (" +
- entry_group.getSequenceLength () / gene_count +
+ buffer.append(" density: " +
+ 1000000L * gene_count /
+ entry_group.getSequenceLength() / 1000.0 +
+ " genes per kb (" +
+ entry_group.getSequenceLength() / gene_count +
" bases per gene)\n");
- buffer.append (" average length: " +
- gene_bases_count / gene_count + "\n");
- buffer.append (" average length (including introns): " +
- gene_bases_count_with_introns / gene_count + "\n");
- buffer.append (" coding percentage: " +
- 1000L * gene_bases_count /
- entry_group.getSequenceLength () / 10.0 + "\n");
- buffer.append (" coding percentage (including introns): " +
- 1000L * gene_bases_count_with_introns /
- entry_group.getSequenceLength () / 10.0 + "\n\n");
-
- buffer.append (" gene sequence composition:\n\n");
+ buffer.append(" average length: " +
+ gene_bases_count / gene_count + "\n");
+ buffer.append(" average length (including introns): " +
+ gene_bases_count_with_introns / gene_count + "\n");
+ buffer.append(" coding percentage: " +
+ 1000L * gene_bases_count /
+ entry_group.getSequenceLength() / 10.0 + "\n");
+ buffer.append(" coding percentage (including introns): " +
+ 1000L * gene_bases_count_with_introns /
+ entry_group.getSequenceLength() / 10.0 + "\n\n");
+
+ buffer.append(" gene sequence composition:\n\n");
final StringVector gene_base_summary =
- SelectionViewer.getBaseSummary (gene_bases);
+ SelectionViewer.getBaseSummary(gene_bases);
- for (int i = 0 ; i < gene_base_summary.size () ; ++i) {
- buffer.append (" ");
- buffer.append (gene_base_summary.elementAt (i)).append ("\n");
+ for(int i = 0 ; i < gene_base_summary.size() ; ++i)
+ {
+ buffer.append(" ");
+ buffer.append(gene_base_summary.elementAt(i)).append("\n");
}
- buffer.append ("\n");
+ buffer.append("\n");
}
- if (pseudo_gene_count > 0) {
- buffer.append ("Pseudo genes (CDS features with a /pseudo " +
- "qualifier):\n");
+ if(pseudo_gene_count > 0)
+ {
+ buffer.append("Pseudo genes (CDS features with a /pseudo " +
+ "qualifier):\n");
- buffer.append (" count: " + pseudo_gene_count + "\n");
- buffer.append (" bases: " + pseudo_gene_bases_count + "\n");
- buffer.append (" average length: " +
- pseudo_gene_bases_count / pseudo_gene_count + "\n\n");
+ buffer.append(" count: " + pseudo_gene_count + "\n");
+ buffer.append(" bases: " + pseudo_gene_bases_count + "\n");
+ buffer.append(" average length: " +
+ pseudo_gene_bases_count / pseudo_gene_count + "\n\n");
}
- if (pseudo_gene_count > 0) {
- buffer.append ("All CDS features:\n");
-
- buffer.append (" count: " + cds_count + "\n");
- buffer.append (" bases: " + cds_bases_count + "\n");
- buffer.append (" average length: " +
- cds_bases_count / cds_count + "\n\n");
+ if(pseudo_gene_count > 0)
+ {
+ buffer.append("All CDS features:\n");
+ buffer.append(" count: " + cds_count + "\n");
+ buffer.append(" bases: " + cds_bases_count + "\n");
+ buffer.append(" average length: " +
+ cds_bases_count / cds_count + "\n\n");
}
}
final Strand strand;
- if (strand_flag == FORWARD || strand_flag == BOTH) {
- strand = entry_group.getBases ().getForwardStrand ();
- } else {
- strand = entry_group.getBases ().getReverseStrand ();
- }
+ if(strand_flag == Bases.FORWARD || strand_flag == BOTH)
+ strand = entry_group.getBases().getForwardStrand();
+ else
+ strand = entry_group.getBases().getReverseStrand();
final StringVector base_summary =
- SelectionViewer.getBaseSummary (strand.getStrandBases ());
+ SelectionViewer.getBaseSummary(strand.getStrandBases());
- buffer.append ("\nOverall sequence composition:\n\n");
+ buffer.append("\nOverall sequence composition:\n\n");
- for (int i = 0 ; i < base_summary.size () ; ++i) {
- buffer.append (base_summary.elementAt (i)).append ("\n");
- }
+ for(int i = 0 ; i < base_summary.size() ; ++i)
+ buffer.append(base_summary.elementAt(i)).append("\n");
- buffer.append ("\nSummary of the active entries:\n");
+ buffer.append("\nSummary of the active entries:\n");
- final Enumeration e = table.keys ();
+ final Enumeration e = table.keys();
- while (e.hasMoreElements()) {
- final String this_key = (String) e.nextElement();
- final Hashtable colour_table = (Hashtable) table.get (this_key);
+ while(e.hasMoreElements())
+ {
+ final String this_key = (String)e.nextElement();
+ final Hashtable colour_table = (Hashtable)table.get(this_key);
- buffer.append (this_key + ": ");
+ buffer.append(this_key + ": ");
- final StringBuffer colour_string = new StringBuffer ();
+ final StringBuffer colour_string = new StringBuffer();
- final Enumeration colour_enum = colour_table.keys ();
+ final Enumeration colour_enum = colour_table.keys();
int total = 0;
- while (colour_enum.hasMoreElements()) {
+ while(colour_enum.hasMoreElements())
+ {
final String this_colour = (String) colour_enum.nextElement();
final int colour_count =
- ((Integer) colour_table.get (this_colour)).intValue ();
+ ((Integer) colour_table.get(this_colour)).intValue();
total += colour_count;
final String end_string;
- if (this_colour.equals ("no colour")) {
+ if(this_colour.equals("no colour"))
end_string = "no colour";
- } else {
+ else
end_string = "colour: " + this_colour;
- }
- if (colour_count == 1) {
- colour_string.append (" one has " + end_string + "\n");
- } else {
- colour_string.append (" " + colour_count + " have " +
- end_string + "\n");
- }
+ if(colour_count == 1)
+ colour_string.append(" one has " + end_string + "\n");
+ else
+ colour_string.append(" " + colour_count + " have " +
+ end_string + "\n");
}
- buffer.append (total + "\n");
-
- buffer.append (colour_string);
+ buffer.append(total + "\n");
+ buffer.append(colour_string);
}
- file_viewer.setText (buffer.toString ());
+ file_viewer.setText(buffer.toString());
}
/**
diff --git a/uk/ac/sanger/artemis/components/ViewMenu.java b/uk/ac/sanger/artemis/components/ViewMenu.java
index f39c5c918e517004d126bbb1b16f7890573c4ac5..4b04a62f2112f33ed64ec21caf1f5ee6307d639f 100644
--- a/uk/ac/sanger/artemis/components/ViewMenu.java
+++ b/uk/ac/sanger/artemis/components/ViewMenu.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ViewMenu.java,v 1.1 2004-06-09 09:47:58 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ViewMenu.java,v 1.2 2004-12-14 15:53:11 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -45,7 +45,7 @@ import javax.swing.*;
* A popup menu with viewing commands.
*
* @author Kim Rutherford
- * @version $Id: ViewMenu.java,v 1.1 2004-06-09 09:47:58 tjc Exp $
+ * @version $Id: ViewMenu.java,v 1.2 2004-12-14 15:53:11 tjc Exp $
**/
public class ViewMenu extends SelectionMenu {
@@ -148,7 +148,7 @@ public class ViewMenu extends SelectionMenu {
forward_overview_item.addActionListener (new ActionListener () {
public void actionPerformed (ActionEvent event) {
new EntryGroupInfoDisplay (getParentFrame (), entry_group,
- EntryGroupInfoDisplay.FORWARD);
+ Bases.FORWARD);
}
});
@@ -156,7 +156,7 @@ public class ViewMenu extends SelectionMenu {
reverse_overview_item.addActionListener (new ActionListener () {
public void actionPerformed (ActionEvent event) {
new EntryGroupInfoDisplay (getParentFrame (), entry_group,
- EntryGroupInfoDisplay.REVERSE);
+ Bases.REVERSE);
}
});