diff --git a/uk/ac/sanger/artemis/components/AlignmentViewer.java b/uk/ac/sanger/artemis/components/AlignmentViewer.java
index 19666975697068eea1cd7a757948defd32395d60..ddd11457c51a32772213f8b193517150e6d3ba72 100644
--- a/uk/ac/sanger/artemis/components/AlignmentViewer.java
+++ b/uk/ac/sanger/artemis/components/AlignmentViewer.java
@@ -102,18 +102,6 @@ public class AlignmentViewer extends CanvasPanel
**/
private Strand orig_query_forward_strand;
- /**
- * Set by the constructor to be the original reverse strand for the subject
- * sequence.
- **/
- private Strand orig_subject_reverse_strand;
-
- /**
- * Set by the constructor to be the original reverse strand for the query
- * sequence.
- **/
- private Strand orig_query_reverse_strand;
-
/** One of the two Entry objects that we are comparing. */
final private EntryGroup subject_entry_group;
@@ -126,7 +114,8 @@ public class AlignmentViewer extends CanvasPanel
/**
* The objects that are listening for AlignmentSelectionChangeEvents.
**/
- private Vector selection_change_listeners = new Vector();
+ private Vector<AlignmentSelectionChangeListener> selection_change_listeners =
+ new Vector<AlignmentSelectionChangeListener>();
/**
* The number of shades of red and blue to use for percentage ID colouring.
@@ -171,8 +160,7 @@ public class AlignmentViewer extends CanvasPanel
private boolean ignore_self_match_flag = false;
/** Vector of those objects that are listening for AlignmentEvents */
- private java.util.Vector alignment_event_listeners =
- new java.util.Vector ();
+ private Vector<AlignmentListener> alignment_event_listeners = new Vector<AlignmentListener> ();
/**
* If true then the FeatureDisplays above and below this AlignmentViewer
@@ -866,19 +854,17 @@ public class AlignmentViewer extends CanvasPanel
**/
public void alignAt(final AlignMatch align_match)
{
- final java.util.Vector targets;
+ final Vector<AlignmentListener> targets;
// copied from a book - synchronizing the whole method might cause a
// deadlock
synchronized(this)
{
- targets = (java.util.Vector)alignment_event_listeners.clone();
+ targets = new Vector<AlignmentListener>(alignment_event_listeners);
}
for(int i = 0; i < targets.size(); ++i)
{
- final AlignmentListener listener =
- (AlignmentListener)targets.elementAt(i);
-
+ final AlignmentListener listener = targets.elementAt(i);
listener.alignMatchChosen(new AlignmentEvent(align_match));
}
}
@@ -1019,9 +1005,7 @@ public class AlignmentViewer extends CanvasPanel
final AlignmentSelectionChangeEvent ev =
new AlignmentSelectionChangeEvent(this, matches);
- final AlignmentSelectionChangeListener listener =
- (AlignmentSelectionChangeListener)selection_change_listeners.elementAt(i);
-
+ final AlignmentSelectionChangeListener listener = selection_change_listeners.elementAt(i);
listener.alignmentSelectionChanged(ev);
}
@@ -1539,7 +1523,7 @@ public class AlignmentViewer extends CanvasPanel
* sequences. If the reverse_position argument is true reverse the
* complemented match coordinates will be returned.
**/
- static int getRealSubjectSequenceStart(final AlignMatch match,
+ protected static int getRealSubjectSequenceStart(final AlignMatch match,
final int sequence_length,
final boolean reverse_position)
{
@@ -1555,7 +1539,7 @@ public class AlignmentViewer extends CanvasPanel
* reverse_position argument is true reverse the complemented match
* coordinates will be returned.
**/
- static int getRealSubjectSequenceEnd(final AlignMatch match,
+ protected static int getRealSubjectSequenceEnd(final AlignMatch match,
final int sequence_length,
final boolean reverse_position)
{
@@ -1571,7 +1555,7 @@ public class AlignmentViewer extends CanvasPanel
* reverse_position argument is true reverse the complemented match
* coordinates will be returned.
**/
- static int getRealQuerySequenceStart(final AlignMatch match,
+ protected static int getRealQuerySequenceStart(final AlignMatch match,
final int sequence_length,
final boolean reverse_position)
{
@@ -1587,7 +1571,7 @@ public class AlignmentViewer extends CanvasPanel
* reverse_position argument is true reverse the complemented match
* coordinates will be returned.
**/
- static int getRealQuerySequenceEnd(final AlignMatch match,
+ protected static int getRealQuerySequenceEnd(final AlignMatch match,
final int sequence_length,
final boolean reverse_position)
{
@@ -1601,7 +1585,7 @@ public class AlignmentViewer extends CanvasPanel
* Remove AlignMatch from the all_matches array
* @param collection of indexes to be removed from the array
*/
- private void removeMatches(Vector index)
+ private void removeMatches(Vector<Integer> index)
{
AlignMatch tmp_matches[] = new AlignMatch[all_matches.length - index.size()];
int start_old = 0;
@@ -1609,7 +1593,7 @@ public class AlignmentViewer extends CanvasPanel
for(int i=0; i<index.size(); i++)
{
- curr_index = ( (Integer)index.get(i) ).intValue();
+ curr_index = ( index.get(i) ).intValue();
if(curr_index !=0)
System.arraycopy(all_matches, start_old, tmp_matches,
@@ -1648,8 +1632,8 @@ public class AlignmentViewer extends CanvasPanel
int split_at;
int delete_overlaps = -1;
- Vector matches_to_split = new Vector();
- Vector removals = new Vector();
+ Vector<Integer> matches_to_split = new Vector<Integer>();
+ Vector<Integer> removals = new Vector<Integer>();
for(int i=0; i<all_matches.length; i++)
{
@@ -1710,7 +1694,7 @@ public class AlignmentViewer extends CanvasPanel
for(int i=0; i<matches_to_split.size(); i++)
{
- curr_index = ((Integer)matches_to_split.get(i)).intValue();
+ curr_index = matches_to_split.get(i).intValue();
//
if(subject)
@@ -1851,7 +1835,7 @@ public class AlignmentViewer extends CanvasPanel
int match_start;
int match_end;
int delete_overlaps = -1;
- Vector removals = new Vector();
+ Vector<Integer> removals = new Vector<Integer>();
for(int i = 0; i < all_matches.length; ++i)
{
@@ -1926,7 +1910,7 @@ public class AlignmentViewer extends CanvasPanel
* no matches.
*
*/
- protected Vector getDifferenceCoords(boolean subject)
+ protected Vector<Integer[]> getDifferenceCoords(boolean subject)
{
final int length;
final boolean flipped;
@@ -1944,7 +1928,6 @@ public class AlignmentViewer extends CanvasPanel
AlignMatchComparator comparator = new AlignMatchComparator(subject, length,
flipped);
-
int imatch = 0;
final AlignMatch[] sorted_all_matches = new AlignMatch[all_matches.length];
for(int i = 0; i < sorted_all_matches.length; ++i)
@@ -1957,7 +1940,7 @@ public class AlignmentViewer extends CanvasPanel
Arrays.sort(sorted_all_matches, 0, imatch, comparator);
int start = 1;
- Vector differences = new Vector();
+ Vector<Integer[]> differences = new Vector<Integer[]>();
// find & record regions of no match
for(int i = 0; i < imatch; ++i)
@@ -2179,7 +2162,7 @@ public class AlignmentViewer extends CanvasPanel
/**
* Return the reference of the subject FeatureDisplay.
**/
- public FeatureDisplay getSubjectDisplay()
+ private FeatureDisplay getSubjectDisplay()
{
return subject_feature_display;
}
@@ -2187,7 +2170,7 @@ public class AlignmentViewer extends CanvasPanel
/**
* Return the reference of the query FeatureDisplay.
**/
- public FeatureDisplay getQueryDisplay()
+ private FeatureDisplay getQueryDisplay()
{
return query_feature_display;
}
@@ -2226,7 +2209,7 @@ public class AlignmentViewer extends CanvasPanel
* Return the forward Strand of the subject EntryGroup from when the
* Comparator was created.
**/
- public Strand getOrigSubjectForwardStrand()
+ private Strand getOrigSubjectForwardStrand()
{
return orig_subject_forward_strand;
}
@@ -2235,29 +2218,11 @@ public class AlignmentViewer extends CanvasPanel
* Return the forward Strand of the query EntryGroup from when the
* Comparator was created.
**/
- public Strand getOrigQueryForwardStrand()
+ private Strand getOrigQueryForwardStrand()
{
return orig_query_forward_strand;
}
- /**
- * Return the reverse Strand of the subject EntryGroup from when the
- * Comparator was created.
- **/
- public Strand getOrigSubjectReverseStrand()
- {
- return orig_subject_reverse_strand;
- }
-
- /**
- * Return the reverse Strand of the query EntryGroup from when the
- * Comparator was created.
- **/
- public Strand getOrigQueryReverseStrand()
- {
- return orig_query_reverse_strand;
- }
-
/**
* Arrange for the two FeatureDisplay objects to scroll in parallel.
**/
@@ -2354,7 +2319,7 @@ public class AlignmentViewer extends CanvasPanel
return comparison_data;
}
- public class AlignMatchComparator implements Comparator
+ public class AlignMatchComparator implements Comparator<AlignMatch>
{
final private boolean subject;
final private int length;
@@ -2368,24 +2333,8 @@ public class AlignmentViewer extends CanvasPanel
this.flipped = flipped;
}
- public int compare(Object o1,Object o2) throws ClassCastException
- {
-// if(o1 == null && o2 == null)
-// return 0;
-// else if (o1 == null)
-// return 1;
-// else if (o2 == null)
-// return -1;
-
- if(!(o1 instanceof AlignMatch))
- throw new ClassCastException();
-
- if(!(o2 instanceof AlignMatch))
- throw new ClassCastException();
-
- AlignMatch c1 = (AlignMatch)o1;
- AlignMatch c2 = (AlignMatch)o2;
-
+ public int compare(AlignMatch c1,AlignMatch c2) throws ClassCastException
+ {
int start1;
int start2;
@@ -2482,14 +2431,12 @@ public class AlignmentViewer extends CanvasPanel
private void colourBox()
{
- //Dimension d = new Dimension(20, 35);
for(int i = 0; i < NUMBER_OF_SHADES; ++i)
{
banner[i].setBackground(definedColour[i]);
banner[i].repaint();
}
}
-
/**
* Return an array of colours that will be used for colouring the matches
@@ -2522,5 +2469,4 @@ public class AlignmentViewer extends CanvasPanel
return definedColour;
}
}
-
}