diff --git a/README b/README
index bad513a64641ac58385710e420cc8029d52b2e5b..510968837cbe1843842e5d84208f39e6f5b7ddfb 100644
--- a/README
+++ b/README
@@ -37,7 +37,7 @@ For information on how to get Artemis see this web page:
COPYRIGHT
-Copyright (C) 1998-2011 Genome Research Limited
+Copyright (C) 1998-2013 Genome Research Limited
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
diff --git a/etc/versions b/etc/versions
index 564964bc2e488b2a09c028c2b85628d9be4f72f7..7a91390aebd7492ab4f200248fb9336d18cec1dd 100644
--- a/etc/versions
+++ b/etc/versions
@@ -1,4 +1,4 @@
-Artemis Release 14.2.3
-ACT Release 11.2.3
+Artemis Release 14.2.4
+ACT Release 11.2.4
DNAPlotter Release 1.9
BamView 1.2.7
diff --git a/uk/ac/sanger/artemis/FeatureSegmentVector.java b/uk/ac/sanger/artemis/FeatureSegmentVector.java
index 68765ea951d3978b9cfa34dc657b5de1c9c4f46f..d360cc5da0c8e7e7c60a5616413eb3acb3684209 100644
--- a/uk/ac/sanger/artemis/FeatureSegmentVector.java
+++ b/uk/ac/sanger/artemis/FeatureSegmentVector.java
@@ -25,6 +25,9 @@
package uk.ac.sanger.artemis;
+import java.util.Collections;
+import java.util.Comparator;
+
import uk.ac.sanger.artemis.util.FastVector;
/**
@@ -36,6 +39,12 @@ import uk.ac.sanger.artemis.util.FastVector;
**/
public class FeatureSegmentVector {
+
+ /**
+ * Storage for FeatureSegment objects.
+ */
+ private FastVector vector = new FastVector ();
+
/**
* Create a new vector of FeatureSegment objects.
**/
@@ -146,9 +155,17 @@ public class FeatureSegmentVector {
return_vector.vector = (FastVector) vector.clone ();
return return_vector;
}
+
+ public void sortByPosition() {
+ Collections.sort(vector, new PositionComparator());
+ }
+}
- /**
- * Storage for FeatureSegment objects.
- */
- private FastVector vector = new FastVector ();
+class PositionComparator implements Comparator<FeatureSegment> {
+ public int compare(FeatureSegment s1, FeatureSegment s2) {
+ if(s1.getStart().getPosition() < s2.getStart().getPosition())
+ return -1;
+ else
+ return 1;
+ }
}
diff --git a/uk/ac/sanger/artemis/components/FeatureBaseViewer.java b/uk/ac/sanger/artemis/components/FeatureBaseViewer.java
index 33d058de29a7455921d1d74f1e592231eca55384..5e08129f5ffcf5ad71f509f2a2da25d987c16a9f 100644
--- a/uk/ac/sanger/artemis/components/FeatureBaseViewer.java
+++ b/uk/ac/sanger/artemis/components/FeatureBaseViewer.java
@@ -25,16 +25,16 @@
package uk.ac.sanger.artemis.components;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+
import uk.ac.sanger.artemis.*;
-import java.awt.event.*;
/**
- * A component for viewing the bases of a feature. Once created this
+ * A component for viewing the bases of a feature. Once created this
* component listens for FeatureChange events to keep the the sequence up to
* date.
- *
* @author Kim Rutherford
- * @version $Id: FeatureBaseViewer.java,v 1.2 2008-12-16 11:46:15 tjc Exp $
**/
public class FeatureBaseViewer
@@ -49,6 +49,8 @@ public class FeatureBaseViewer
/** The Entry that contains the Feature this object is displaying. */
private Entry entry;
+ private FeatureSegmentVector segments;
+
/**
* Create a new FeatureBaseViewer component to display the bases of the
* given Feature.
@@ -58,10 +60,12 @@ public class FeatureBaseViewer
* sequence).
**/
public FeatureBaseViewer (final Feature feature,
- final boolean include_numbers)
+ final boolean include_numbers,
+ final FeatureSegmentVector segments)
{
this.feature = feature;
this.entry = feature.getEntry ();
+ this.segments = segments;
sequence_viewer =
new SequenceViewer ("Feature base viewer for feature:" +
@@ -126,26 +130,33 @@ public class FeatureBaseViewer
**/
private void redisplay ()
{
- final StringBuffer header_buffer = new StringBuffer();
-
- header_buffer.append(getFeature().getSystematicName());
- header_buffer.append(" ");
- header_buffer.append(getFeature().getIDString());
- header_buffer.append(" ");
-
final String product = getFeature().getProductString();
-
- if(product == null)
- header_buffer.append("undefined product");
- else
- header_buffer.append(product);
-
- header_buffer.append(" ").append(getFeature().getWriteRange());
+ final StringBuilder hdr = new StringBuilder();
+ hdr.append(getFeature().getSystematicName()).append(" ");
+ hdr.append(getFeature().getIDString()).append(" ");
+ hdr.append(product == null ? "undefined product" : product);
- final String comment = ">" + header_buffer.toString();
-
- final String bases = getFeature ().getBases ().toUpperCase ();
- sequence_viewer.setSequence (comment, bases);
+ final String bases;
+ if(segments != null) // display just for selected segments
+ {
+ final StringBuilder buffer = new StringBuilder();
+ segments.sortByPosition();
+ for(int i = 0; i < segments.size(); ++i)
+ {
+ final FeatureSegment segment = segments.elementAt(i);
+ buffer.append(segment.getBases());
+ hdr.append(i == 0 ? " " : ",").append(segment.getRawRange().toString());
+ }
+ hdr.append(getFeature ().isForwardFeature() ? " forward" : " reverse");
+ bases = buffer.toString();
+ }
+ else
+ {
+ hdr.append(" ").append(getFeature().getWriteRange());
+ bases = getFeature ().getBases ();
+ }
+
+ sequence_viewer.setSequence (">" + hdr.toString(), bases.toUpperCase ());
}
/**
diff --git a/uk/ac/sanger/artemis/components/MultiComparator.java b/uk/ac/sanger/artemis/components/MultiComparator.java
index 06a393fb88061a2b83333f2d734681cb74525b34..c412fd8e69ce82af1b2d1edd540a5646b1c51860 100644
--- a/uk/ac/sanger/artemis/components/MultiComparator.java
+++ b/uk/ac/sanger/artemis/components/MultiComparator.java
@@ -301,7 +301,7 @@ public class MultiComparator extends JFrame
if(i < getAlignmentViewerArray().length)
{
c.fill = GridBagConstraints.BOTH;
- c.weighty = 1;
+ c.weighty = 0.5;
getContentPane().add(getAlignmentViewerArray()[i], c);
}
}
diff --git a/uk/ac/sanger/artemis/components/StickyFileChooser.java b/uk/ac/sanger/artemis/components/StickyFileChooser.java
index 96314b5102f7fc55830626477e5637756b33d737..caf1e98c29f506b74d3ddbf061b93fcc67b79cb0 100644
--- a/uk/ac/sanger/artemis/components/StickyFileChooser.java
+++ b/uk/ac/sanger/artemis/components/StickyFileChooser.java
@@ -26,21 +26,18 @@
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.Options;
-
import java.io.File;
import javax.swing.JFileChooser;
import javax.swing.JFrame;
/**
* A JFileChooser that remembers which directory it is in for next time.
- *
- * @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: StickyFileChooser.java,v 1.1 2004-06-09 09:47:49 tjc Exp $
+ * @author Kim Rutherford
**/
public class StickyFileChooser extends JFileChooser
{
-
+ private static final long serialVersionUID = 1L;
/**
* Used to remember the directory the JFileChooser was in when the user
* pressed OK. This is used as the starting directory next time.
diff --git a/uk/ac/sanger/artemis/components/ViewMenu.java b/uk/ac/sanger/artemis/components/ViewMenu.java
index 24e934b54a80ef827bcb43e7660653fb838ac7b8..d86c8114b0f4461b1c85f87b8282bfdb117f653f 100644
--- a/uk/ac/sanger/artemis/components/ViewMenu.java
+++ b/uk/ac/sanger/artemis/components/ViewMenu.java
@@ -143,26 +143,42 @@ public class ViewMenu extends SelectionMenu
}
});
- final JMenuItem view_bases_item = new JMenuItem("Bases Of Selection");
+ final JMenu view_bases = new JMenu("Bases");
+ final JMenuItem view_bases_item = new JMenuItem("Of Selection");
view_bases_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
{
- viewSelectedBases(true);
+ viewSelectedBases(true, false);
}
});
+ view_bases.add(view_bases_item);
final JMenuItem view_bases_as_fasta_item =
- new JMenuItem("Bases Of Selection As FASTA");
+ new JMenuItem("Of Selection As FASTA");
view_bases_as_fasta_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
{
- viewSelectedBases(false);
+ viewSelectedBases(false, false);
}
});
+ view_bases.add(view_bases_as_fasta_item);
+ view_bases.addSeparator();
- final JMenuItem view_aa_item = new JMenuItem("Amino Acids Of Selection");
+ final JMenuItem view_exon_bases =
+ new JMenuItem("Of Selected Exons As FASTA");
+ view_exon_bases.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent event)
+ {
+ viewSelectedBases(false, true);
+ }
+ });
+ view_bases.add(view_exon_bases);
+
+ final JMenu view_aa = new JMenu("Amino Acids");
+ final JMenuItem view_aa_item = new JMenuItem("Of Selection");
view_aa_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -170,9 +186,10 @@ public class ViewMenu extends SelectionMenu
viewSelectedAminoAcids(true);
}
});
+ view_aa.add(view_aa_item);
final JMenuItem view_aa_as_fasta_item =
- new JMenuItem("Amino Acids Of Selection As FASTA");
+ new JMenuItem("Of Selection As FASTA");
view_aa_as_fasta_item.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -180,6 +197,7 @@ public class ViewMenu extends SelectionMenu
viewSelectedAminoAcids(false);
}
});
+ view_aa.add(view_aa_as_fasta_item);
final JMenuItem overview_item = new JMenuItem("Overview");
overview_item.setAccelerator(OVERVIEW_KEY);
@@ -554,10 +572,8 @@ public class ViewMenu extends SelectionMenu
add(forward_overview_item);
add(reverse_overview_item);
addSeparator();
- add(view_bases_item);
- add(view_bases_as_fasta_item);
- add(view_aa_item);
- add(view_aa_as_fasta_item);
+ add(view_bases);
+ add(view_aa);
addSeparator();
add(feature_info_item);
add(plot_features_item);
@@ -1712,32 +1728,36 @@ public class ViewMenu extends SelectionMenu
* (every second line of the display will be numbers rather than
* sequence).
**/
- private void viewSelectedBases (final boolean include_numbers) {
+ private void viewSelectedBases (final boolean include_numbers, final boolean selectedExonsOnly) {
if (getSelection ().isEmpty ()) {
new MessageDialog (getParentFrame (), "Nothing selected");
return;
}
- final MarkerRange range = selection.getMarkerRange ();
+ if (selection.getMarkerRange () == null) {
+ final FeatureVector fs = getSelection ().getAllFeatures ();
- if (range == null) {
- final FeatureVector features_to_view = getSelection ().getAllFeatures ();
-
- if (features_to_view.size () > MAXIMUM_SELECTED_FEATURES) {
- new MessageDialog (getParentFrame (),
- "warning: only viewing bases for " +
- "the first " + MAXIMUM_SELECTED_FEATURES +
- " selected features");
+ if(selectedExonsOnly)
+ {
+ if (fs.size () > 1)
+ new MessageDialog (getParentFrame (),
+ "warning: only viewing bases for the selected exons of one feature");
+ new FeatureBaseViewer (fs.elementAt(0), include_numbers,
+ getSelection ().getSelectedSegments());
}
-
- for (int i = 0 ;
- i < features_to_view.size () && i < MAXIMUM_SELECTED_FEATURES ;
- ++i) {
- final Feature this_feature = features_to_view.elementAt (i);
-
- new FeatureBaseViewer (this_feature, include_numbers);
+ else
+ {
+ if (fs.size () > MAXIMUM_SELECTED_FEATURES)
+ new MessageDialog (getParentFrame (),
+ "warning: only viewing bases for " +
+ "the first " + MAXIMUM_SELECTED_FEATURES +
+ " selected features");
+ for (int i = 0; i < fs.size () && i < MAXIMUM_SELECTED_FEATURES; ++i)
+ new FeatureBaseViewer (fs.elementAt (i), include_numbers, null);
}
- } else {
+ }
+ else
+ {
final SequenceViewer sequence_viewer =
new SequenceViewer ("Selected bases", include_numbers);
diff --git a/uk/ac/sanger/artemis/components/alignment/BamFrame.java b/uk/ac/sanger/artemis/components/alignment/BamFrame.java
index 394836007d8781c4cfe48d5a876a9fc592cd1856..8c23edc383a6460e3f8a7680a35257c2564d7e97 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamFrame.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamFrame.java
@@ -23,7 +23,7 @@ import javax.swing.JOptionPane;
// methods we wish to
// use as delegates for various com.apple.eawt.ApplicationListener
// methods
- Class bamClass = Class.forName("uk.ac.sanger.artemis.components.alignment.BamFrame");
+ Class<?> bamClass = Class.forName("uk.ac.sanger.artemis.components.alignment.BamFrame");
BamOSXAdapter.setQuitHandler(this, bamClass.getDeclaredMethod(
"exitApp", (Class[]) null));
BamOSXAdapter.setAboutHandler(this, bamClass.getDeclaredMethod("about",
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index b576aa4a32c05179e9a8d6f73af27f8b381a5297..93193d7684e69831734b6f8acce3234e82eb1dde 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -2382,7 +2382,7 @@ public class BamView extends JPanel
* @param c
* @return
*/
- protected ImageIcon getImageIcon(Color c)
+ private ImageIcon getImageIcon(Color c)
{
BufferedImage image = (BufferedImage)this.createImage(10, 10);
Graphics2D g2 = image.createGraphics();
diff --git a/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java b/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
index ee720fca2e79606505f59dc3b090db93c605fc19..ebf7c558a9591b70dcd66c3c5d953ed9661c408e 100644
--- a/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
+++ b/uk/ac/sanger/artemis/components/alignment/GroupBamFrame.java
@@ -180,13 +180,9 @@ class GroupBamFrame extends JFrame
c.gridy += 1;
c.gridx = 0;
bamPanel.add(new JLabel(bam), c);
-
- Color col = bamView.getColorByJCheckBoxMenuItem(cbBam);
- if(col == null)
- col = Color.BLACK;
-
+
c.gridx = 1;
- bamPanel.add(new JLabel(bamView.getImageIcon(col)), c);
+ bamPanel.add(new JLabel(cbBam.getIcon()), c);
c.gridx = 2;
JComboBox groupCombo = new JComboBox( groups );
diff --git a/uk/ac/sanger/artemis/components/alignment/ReadCountDialog.java b/uk/ac/sanger/artemis/components/alignment/ReadCountDialog.java
index f1bef0a0ca7c4962f6bc6a70a5b80d7c9ff26243..17861ff9661f76b1165671bfc6f2a98c3e558f24 100644
--- a/uk/ac/sanger/artemis/components/alignment/ReadCountDialog.java
+++ b/uk/ac/sanger/artemis/components/alignment/ReadCountDialog.java
@@ -140,7 +140,7 @@ import uk.ac.sanger.artemis.util.StringVector;
qNames = new StringVector();
Object objs[] = systematicListSelectionPanel.getResultArray();
for(Object o: objs)
- qNames.add(o);
+ qNames.add((String)o);
}
return pickName(f, qNames);
diff --git a/uk/ac/sanger/artemis/components/variant/VCFview.java b/uk/ac/sanger/artemis/components/variant/VCFview.java
index 83220e3e34ef54f64c046ec2346e1a9efd598f8c..31a60edc86b723ecefc2f6fdbfbebe237fb4abf0 100644
--- a/uk/ac/sanger/artemis/components/variant/VCFview.java
+++ b/uk/ac/sanger/artemis/components/variant/VCFview.java
@@ -158,7 +158,7 @@ public class VCFview extends JPanel
private int dragStart = -1;
private JPopupMenu popup;
private JMenu vcfFilesMenu = new JMenu("VCF files");
- private int LINE_HEIGHT = 15;
+ private int LINE_HEIGHT = 14;
protected boolean showSynonymous = true;
protected boolean showNonSynonymous = true;
@@ -262,7 +262,6 @@ public class VCFview extends JPanel
JPanel bottomPanel = new JPanel(new BorderLayout());
graphPanel = new GraphPanel(this);
graphPanel.setBorder(BorderFactory.createMatteBorder(1, 0, 1, 0, Color.gray));
- graphPanel.setPreferredSize(new Dimension(900, 100));
graphPanel.setVisible(false);
bottomPanel.add(graphPanel, BorderLayout.CENTER);
@@ -342,8 +341,31 @@ public class VCFview extends JPanel
for(int i=0; i<vcfFiles.size(); i++)
addToViewMenu(i);
- popup.addSeparator();
+ final JMenu lineHgt = new JMenu("Row Height");
+ popup.add(lineHgt);
+ final ButtonGroup groupLnHgt = new ButtonGroup();
+ for(int i=8; i<37; i+=2)
+ {
+ final int ii = i;
+ final JCheckBoxMenuItem hgtMenu = new JCheckBoxMenuItem(
+ Integer.toString(i), (i == LINE_HEIGHT));
+ groupLnHgt.add(hgtMenu);
+ hgtMenu.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ if(hgtMenu.isSelected())
+ {
+ LINE_HEIGHT = ii;
+ setDisplay();
+ revalidate();
+ }
+ }
+ });
+ lineHgt.add(hgtMenu);
+ }
+ popup.addSeparator();
markNewStops.addActionListener(new ActionListener()
{
@@ -580,7 +602,7 @@ public class VCFview extends JPanel
graphDP.setSelected(false);
graphSim.setSelected(false);
graphPanel.setType(0);
- graphPanel.repaint();
+ setGraphSize();
}
});
@@ -592,7 +614,7 @@ public class VCFview extends JPanel
graphSNP.setSelected(false);
graphSim.setSelected(false);
graphPanel.setType(1);
- graphPanel.repaint();
+ setGraphSize();
}
});
@@ -604,7 +626,7 @@ public class VCFview extends JPanel
graphSNP.setSelected(false);
graphDP.setSelected(false);
graphPanel.setType(2);
- graphPanel.repaint();
+ setGraphSize();
}
});
@@ -643,6 +665,19 @@ public class VCFview extends JPanel
popup.add(labels);
}
+ private void setGraphSize()
+ {
+ repaint();
+ if(graphPanel.isVisible())
+ graphPanel.setPreferredSize(new Dimension(900, 70));
+ else
+ graphPanel.setPreferredSize(new Dimension(900, 1));
+
+ vcfPanel.setPreferredSize(new Dimension(900,
+ graphPanel.getPreferredSize().height+getPreferredSize().height));
+ vcfPanel.revalidate();
+ }
+
private void createTopPanel(final JFrame frame, final EntryEdit entry_edit)
{
final JComponent topPanel;
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index ce33eed6698adcaa6cf2897f2692b32fc9af8f19..162d45f94ae416b43f1538d0d6b5973bd7fae3dc 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -1187,7 +1187,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
new StringTokenizer((String)att_values.get(0), ",");
StringVector str_values = new StringVector();
while(stok.hasMoreTokens())
- str_values.add(stok.nextElement());
+ str_values.add(stok.nextToken());
att_values = str_values;
}
diff --git a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
index 0a69f718add3b0acc61c65572245071d91b9a580..a4e6fc83ee7ab1740b56d16eecc92a77a4a68e89 100644
--- a/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/UserDataAlgorithm.java
@@ -953,13 +953,13 @@ public class UserDataAlgorithm extends BaseAlgorithm
base = Integer.parseInt((String)parts.get(getStartColumn()-1)) - start;
else
{
- int b = Integer.parseInt((String)parts.get(getStartColumn()-1));
- int e = Integer.parseInt((String)parts.get(getEndColumn()-1));
+ int b = Integer.parseInt(parts.get(getStartColumn()-1));
+ int e = Integer.parseInt(parts.get(getEndColumn()-1));
base = b + ((b - e)/2) - start;
}
for(int i=0; i<rvalues[base].length; i++)
{
- float val = Float.parseFloat( (String) parts.get(i+getEndColumn()) );
+ float val = Float.parseFloat( parts.get(i+getEndColumn()) );
if(logTransform)
val = (float) Math.log(val+1);
diff --git a/uk/ac/sanger/artemis/util/StringVector.java b/uk/ac/sanger/artemis/util/StringVector.java
index 6baecc33ec338f263ca6d01ee44ab6694088d61b..95f560d579a90ea74c2f1060d6a6e1bb08440016 100644
--- a/uk/ac/sanger/artemis/util/StringVector.java
+++ b/uk/ac/sanger/artemis/util/StringVector.java
@@ -36,8 +36,10 @@ import java.util.Comparator;
* @version $Id: StringVector.java,v 1.5 2005-10-13 12:06:12 tjc Exp $
**/
-public class StringVector extends Vector
+public class StringVector extends Vector<String>
{
+ private static final long serialVersionUID = 1L;
+
/**
* Create a new vector of String objects.
**/
@@ -85,10 +87,10 @@ public class StringVector extends Vector
* package.
*/
public void sort()
- {
- final Comparator comparator = new Comparator()
+ {
+ final Comparator<String> comparator = new Comparator<String>()
{
- public int compare(Object fst, Object snd)
+ public int compare(String fst, String snd)
{
if(fst == null)
{
@@ -102,7 +104,7 @@ public class StringVector extends Vector
if(snd == null)
return 1;
}
- return ((String)fst).compareTo((String) snd);
+ return fst.compareTo(snd);
}
};
@@ -122,61 +124,59 @@ public class StringVector extends Vector
* splitting using the given characters. If the argument String is zero
* length or it consists only of the characters used to split, the return
* vector will be zero length.
- * @param keep_zero_char_tokens If true then zero width tokens will be
- * returned. eg. when spliting on tabs if this parameter is true then
+ * @param keep_zero_char_toks If true then zero width tokens will be
+ * returned. eg. when splitting on tabs if this parameter is true then
* splitting this "\t\tfoo" will return "" and "foo". If this flag is
* false then the split_characters will be treated as a block (and "foo"
* would be returned in the example.
**/
public static StringVector getStrings(final String argument,
- String split_characters,
- final boolean keep_zero_char_tokens)
+ final String delim,
+ final boolean keep_zero_char_toks)
{
- final StringVector return_vector = new StringVector();
+ final StringVector strVector = new StringVector();
- String value;
- String last_value = null;
+ String tok;
+ String lastTok = null;
+ int idx1 = 0;
+ int idx2;
+ final int argLen = argument.length();
- int ind1 = 0;
- int ind2;
- int argLen = argument.length();
-
- while(ind1 < argLen)
+ while(idx1 < argLen)
{
- ind2 = argument.indexOf(split_characters,ind1);
- if(ind2 == ind1)
+ idx2 = argument.indexOf(delim,idx1);
+ if(idx2 == idx1)
{
- ind1++;
+ idx1++;
continue;
}
- if(ind2 < 0)
- ind2 = argLen;
+ if(idx2 < 0)
+ idx2 = argLen;
- value = argument.substring(ind1,ind2);
- ind1 = ind2+1;
+ tok = argument.substring(idx1,idx2);
+ idx1 = idx2+1;
- if(value.length() == 1 &&
- split_characters.indexOf(value.charAt(0)) != -1)
+ if(tok.length() == 1 &&
+ delim.indexOf(tok.charAt(0)) != -1)
{
// ignore the split characters
-
- if(keep_zero_char_tokens &&
- (last_value == null ||
- last_value != null && last_value.length () == 1 &&
- split_characters.indexOf (last_value) != -1))
+ if(keep_zero_char_toks &&
+ (lastTok == null ||
+ lastTok != null && lastTok.length () == 1 &&
+ delim.indexOf (lastTok) != -1))
{
- // we need to add a space because of two split_characters in a row
- return_vector.add("");
+ // add a space because of two split_characters in a row
+ strVector.add("");
}
}
else
- return_vector.add(value);
+ strVector.add(tok);
- last_value = value;
+ lastTok = tok;
}
- return return_vector;
+ return strVector;
}
/**
@@ -207,13 +207,19 @@ public class StringVector extends Vector
{
String argument = "a a g g g c a c g t c g c a t c g a c t c";
long startTime = System.currentTimeMillis();
-
for(int i=0; i<10000000; i++)
getStrings(argument, " ", true);
- long endTime = System.currentTimeMillis();
+ System.out.println("TIME TAKEN "+ Long.toString(System.currentTimeMillis()-startTime));
- System.out.println("TIME TAKEN "+ Long.toString(endTime-startTime));
+ startTime = System.currentTimeMillis();
+ for(int i=0; i<10000000; i++)
+ {
+ java.util.StringTokenizer st = new java.util.StringTokenizer(argument, " ", true);
+ while(st.hasMoreTokens())
+ st.nextToken();
+ }
+ System.out.println("TIME TAKEN "+ Long.toString(System.currentTimeMillis()-startTime));
}
}
diff --git a/uk/ac/sanger/artemis/util/TextDocument.java b/uk/ac/sanger/artemis/util/TextDocument.java
index 8955b44d75ca4af22efbe631980e9fa498a17482..2ceee5bab7e4af175de2e9e3bf1c1ab91f411d18 100644
--- a/uk/ac/sanger/artemis/util/TextDocument.java
+++ b/uk/ac/sanger/artemis/util/TextDocument.java
@@ -24,25 +24,28 @@
package uk.ac.sanger.artemis.util;
-import java.io.*;
import javax.swing.JOptionPane;
-import uk.ac.sanger.artemis.components.SwingWorker;
import java.awt.Toolkit;
-import java.awt.datatransfer.*;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.Transferable;
+import java.awt.datatransfer.UnsupportedFlavorException;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
/**
* Objects of this class are Documents created from a file.
- *
**/
-
public class TextDocument extends Document
{
/**
- *
* Create a new TextDocument from a String.
* @param location This should be a file or directory name.
* @param remote_file File on server
- *
**/
public TextDocument()
{
@@ -169,35 +172,4 @@ public class TextDocument extends Document
return file_output_stream;
}
- /**
- *
- * Save the entry back to the ssh server
- *
- */
-/*
- public void saveEntry(final File local_file)
- {
- SwingWorker putWorker = new SwingWorker()
- {
- FileTransferProgressMonitor monitor;
- public Object construct()
- {
- monitor = new FileTransferProgressMonitor(null);
- FTProgress progress = monitor.add(local_file.getName());
-
- getRemoteFileNode().put(local_file, progress);
- monitor.close();
- return null;
- }
-
- public void finished()
- {
- if(monitor != null)
- monitor.close();
- }
- };
- putWorker.start();
- }
-*/
-
}