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(JAL-969) refactored alignmentViewport base class to own package and pulled up most...
[jalview.git]
/
src
/
jalview
/
datamodel
/
AlignmentView.java
diff --git
a/src/jalview/datamodel/AlignmentView.java
b/src/jalview/datamodel/AlignmentView.java
index
0b4e236
..
8e596ce
100644
(file)
--- a/
src/jalview/datamodel/AlignmentView.java
+++ b/
src/jalview/datamodel/AlignmentView.java
@@
-1,6
+1,6
@@
/*
\r
/*
\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
\r
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
\r
*
\r
* This file is part of Jalview.
\r
*
\r
*
\r
* This file is part of Jalview.
\r
*
\r
@@
-107,7
+107,7
@@
public class AlignmentView
{
\r
Vector sel = selection.getSequences(null);
\r
this.selected = new Vector();
\r
{
\r
Vector sel = selection.getSequences(null);
\r
this.selected = new Vector();
\r
- selseqs = selection.getSequencesInOrder(alignment, false);
\r
+ selseqs = selection.getSequencesInOrder(alignment, selectedRegionOnly);
\r
}
\r
else
\r
{
\r
}
\r
else
\r
{
\r
@@
-115,7
+115,13
@@
public class AlignmentView
}
\r
\r
// get the alignment's group list and make a copy
\r
}
\r
\r
// get the alignment's group list and make a copy
\r
- Vector grps = new Vector(alignment.getGroups());
\r
+ Vector grps = new Vector();
\r
+ Vector gg = alignment.getGroups();
\r
+ Enumeration gge = gg.elements();
\r
+ while (gge.hasMoreElements())
\r
+ {
\r
+ grps.addElement(gge.nextElement());
\r
+ }
\r
ScGroup[] sgrps = null;
\r
boolean addedgps[] = null;
\r
if (grps != null)
\r
ScGroup[] sgrps = null;
\r
boolean addedgps[] = null;
\r
if (grps != null)
\r
@@
-128,7
+134,7
@@
public class AlignmentView
// visible and selected region
\r
int ssel = selection.getStartRes(), esel = selection.getEndRes();
\r
Vector isg = new Vector();
\r
// visible and selected region
\r
int ssel = selection.getStartRes(), esel = selection.getEndRes();
\r
Vector isg = new Vector();
\r
- Enumeration<?> en = grps.elements();
\r
+ Enumeration en = grps.elements();
\r
while (en.hasMoreElements())
\r
{
\r
sg = (SequenceGroup) en.nextElement();
\r
while (en.hasMoreElements())
\r
{
\r
sg = (SequenceGroup) en.nextElement();
\r
@@
-144,6
+150,9
@@
public class AlignmentView
{
\r
sg.setEndRes(esel);
\r
}
\r
{
\r
sg.setEndRes(esel);
\r
}
\r
+ sg.setStartRes(sg.getStartRes()-ssel+1);
\r
+ sg.setEndRes(sg.getEndRes()-ssel+1);
\r
+
\r
isg.addElement(sg);
\r
}
\r
}
\r
isg.addElement(sg);
\r
}
\r
}
\r
@@
-177,7
+186,7
@@
public class AlignmentView
{
\r
for (int sg = 0; sg < sgrps.length; sg++)
\r
{
\r
{
\r
for (int sg = 0; sg < sgrps.length; sg++)
\r
{
\r
- if (((Vector) grps.get(sg)).contains(selseqs[i]))
\r
+ if (((Vector) grps.elementAt(sg)).contains(selseqs[i]))
\r
{
\r
sequences[csi].setGroupMembership(sgrps[sg]);
\r
sgrps[sg].sg.deleteSequence(selseqs[i], false);
\r
{
\r
sequences[csi].setGroupMembership(sgrps[sg]);
\r
sgrps[sg].sg.deleteSequence(selseqs[i], false);
\r
@@
-326,7
+335,7
@@
public class AlignmentView
* prune any groups to the visible coordinates of the alignment.
\r
*/
\r
{
\r
* prune any groups to the visible coordinates of the alignment.
\r
*/
\r
{
\r
- int nvg = scGroups != null ? scGroups.size() : 0;
\r
+ int nvg = (scGroups != null) ? scGroups.size() : 0;
\r
if (nvg > 0)
\r
{
\r
SequenceGroup[] nsg = new SequenceGroup[nvg];
\r
if (nvg > 0)
\r
{
\r
SequenceGroup[] nsg = new SequenceGroup[nvg];
\r
@@
-342,9
+351,14
@@
public class AlignmentView
continue;
\r
}
\r
}
\r
continue;
\r
}
\r
}
\r
+
\r
+ // clone group properties
\r
+ nsg[g] = new SequenceGroup(sg);
\r
+
\r
// may need to shift/trim start and end ?
\r
if (r && !viscontigs)
\r
{
\r
// may need to shift/trim start and end ?
\r
if (r && !viscontigs)
\r
{
\r
+ // Not fully tested code - routine not yet called with viscontigs==false
\r
if (nsg[g].getStartRes() < gstart)
\r
{
\r
nsg[g].setStartRes(0);
\r
if (nsg[g].getStartRes() < gstart)
\r
{
\r
nsg[g].setStartRes(0);
\r
@@
-354,14
+368,11
@@
public class AlignmentView
nsg[g].setStartRes(nsg[g].getStartRes() - gstart);
\r
nsg[g].setEndRes(nsg[g].getEndRes() - gstart);
\r
}
\r
nsg[g].setStartRes(nsg[g].getStartRes() - gstart);
\r
nsg[g].setEndRes(nsg[g].getEndRes() - gstart);
\r
}
\r
- if (nsg[g].getEndRes() > gend)
\r
+ if (nsg[g].getEndRes() > (gend-gstart))
\r
{
\r
{
\r
- nsg[g].setEndRes(gend);
\r
+ nsg[g].setEndRes(gend-gstart);
\r
}
\r
}
\r
}
\r
}
\r
-
\r
- // clone group properties
\r
- nsg[g] = new SequenceGroup(sg);
\r
}
\r
if (viscontigs)
\r
{
\r
}
\r
if (viscontigs)
\r
{
\r
@@
-983,9
+994,13
@@
public class AlignmentView
public static void summariseAlignmentView(AlignmentView view,
\r
PrintStream os)
\r
{
\r
public static void summariseAlignmentView(AlignmentView view,
\r
PrintStream os)
\r
{
\r
- os.println("View has " + view.sequences.length + " of which "
\r
- + (view.selected == null ? "None" : view.selected.size())
\r
- + " are selected.");
\r
+ os.print("View has " + view.sequences.length + " of which ");
\r
+ if (view.selected == null) {
\r
+ os.print("None");
\r
+ } else {
\r
+ os.print(" "+view.selected.size());
\r
+ }
\r
+ os.println(" are selected.");
\r
os.print("View is " + view.getWidth() + " columns wide");
\r
int viswid = 0;
\r
int[] contigs = view.getContigs();
\r
os.print("View is " + view.getWidth() + " columns wide");
\r
int viswid = 0;
\r
int[] contigs = view.getContigs();
\r