X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=de4d979cbb51029be351892c43906e5e6424847a;hb=47c72d35e5716a194ef2396cd1e6b81a91cbb0ea;hp=e6ed8f295dbfa9c5ee61026ca85cd2fb59c749c2;hpb=caf13e6a9dc82023cd8648420201e5ad60ce0393;p=jalview.git
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
old mode 100755
new mode 100644
index e6ed8f2..de4d979
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -1,19 +1,22 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
@@ -28,6 +31,7 @@ import jalview.schemes.*;
import jalview.structure.SelectionSource;
import jalview.structure.SequenceListener;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
public class SeqPanel extends Panel implements MouseMotionListener,
MouseListener, SequenceListener
@@ -91,7 +95,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
seqCanvas.addMouseMotionListener(this);
seqCanvas.addMouseListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager();
+ ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
ssm.addStructureViewerListener(this);
seqCanvas.repaint();
@@ -146,7 +150,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
seqCanvas.cursorY);
- seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
scrollToVisible();
}
@@ -154,19 +158,20 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
- if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+ if (av.hasHiddenColumns()
+ && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
- int maxWidth = av.alignment.getWidth();
+ int maxWidth = av.getAlignment().getWidth();
- while (!av.colSel.isVisible(seqCanvas.cursorX)
+ while (!av.getColumnSelection().isVisible(seqCanvas.cursorX)
&& seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
{
seqCanvas.cursorX += dx;
}
if (seqCanvas.cursorX >= maxWidth
- || !av.colSel.isVisible(seqCanvas.cursorX))
+ || !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
seqCanvas.cursorX = original;
}
@@ -180,18 +185,18 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
seqCanvas.cursorX = 0;
}
- else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+ else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
{
- seqCanvas.cursorX = av.alignment.getWidth() - 1;
+ seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
}
if (seqCanvas.cursorY < 0)
{
seqCanvas.cursorY = 0;
}
- else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+ else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
{
- seqCanvas.cursorY = av.alignment.getHeight() - 1;
+ seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
}
endEditing();
@@ -209,7 +214,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
ap.scrollUp(false);
}
- while (seqCanvas.cursorX < av.colSel
+ while (seqCanvas.cursorX < av.getColumnSelection()
.adjustForHiddenColumns(av.startRes))
{
@@ -218,7 +223,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
break;
}
}
- while (seqCanvas.cursorX > av.colSel
+ while (seqCanvas.cursorX > av.getColumnSelection()
.adjustForHiddenColumns(av.endRes))
{
if (!ap.scrollRight(true))
@@ -227,7 +232,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
}
}
- setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+ setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
seqCanvas.repaint();
@@ -240,12 +245,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
if (av.getSelectionGroup() != null)
{
- SequenceGroup sg = av.selectionGroup;
+ SequenceGroup sg = av.getSelectionGroup();
// Find the top and bottom of this group
- int min = av.alignment.getHeight(), max = 0;
+ int min = av.getAlignment().getHeight(), max = 0;
for (int i = 0; i < sg.getSize(); i++)
{
- int index = av.alignment.findIndex(sg.getSequenceAt(i));
+ int index = av.getAlignment().findIndex(sg.getSequenceAt(i));
if (index > max)
{
max = index;
@@ -287,10 +292,10 @@ public class SeqPanel extends Panel implements MouseMotionListener,
else
{
// Now add any sequences between min and max
- sg.getSequences(null).removeAllElements();
+ sg.clear();
for (int i = min; i < max; i++)
{
- sg.addSequence(av.alignment.getSequenceAt(i), false);
+ sg.addSequence(av.getAlignment().getSequenceAt(i), false);
}
}
}
@@ -344,26 +349,36 @@ public class SeqPanel extends Panel implements MouseMotionListener,
int getKeyboardNo1()
{
- if (keyboardNo1 == null)
- return 1;
- else
+ try
+ {
+ if (keyboardNo1 != null)
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
+ } catch (Exception x)
{
- int value = Integer.parseInt(keyboardNo1.toString());
- keyboardNo1 = null;
- return value;
}
+ keyboardNo1 = null;
+ return 1;
}
int getKeyboardNo2()
{
- if (keyboardNo2 == null)
- return 1;
- else
+ try
+ {
+ if (keyboardNo2 != null)
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
+ } catch (Exception x)
{
- int value = Integer.parseInt(keyboardNo2.toString());
- keyboardNo2 = null;
- return value;
}
+ keyboardNo2 = null;
+ return 1;
}
void setStatusMessage(SequenceI sequence, int res, int seq)
@@ -372,7 +387,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
+ sequence.getName());
Object obj = null;
- if (av.alignment.isNucleotide())
+ if (av.getAlignment().isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ "");
@@ -455,10 +470,11 @@ public class SeqPanel extends Panel implements MouseMotionListener,
public void mouseClicked(MouseEvent evt)
{
- SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+ SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
if (evt.getClickCount() > 1)
{
- if (av.getSelectionGroup().getSize() == 1
+ if (av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() == 1
&& av.getSelectionGroup().getEndRes()
- av.getSelectionGroup().getStartRes() < 2)
{
@@ -543,7 +559,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
res = (x / av.getCharWidth()) + av.getStartRes();
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
@@ -581,8 +597,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(),
- av.alignment.getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
+ .getHeight() - 1);
if (seq < 0)
{
seq = -1;
@@ -590,8 +606,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
else
{
- seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
- av.alignment.getHeight() - 1);
+ seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+ .getAlignment().getHeight() - 1);
if (seq < 0)
{
seq = -1;
@@ -639,11 +655,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
public void highlightSequence(SearchResults results)
{
- seqCanvas.highlightSearchResults(results);
if (av.followHighlight)
{
- ap.scrollToPosition(results);
+ if (ap.scrollToPosition(results, true))
+ {
+ ap.alignFrame.repaint();
+ }
}
+ seqCanvas.highlightSearchResults(results);
+
}
public void updateColours(SequenceI seq, int index)
@@ -684,7 +704,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
+ sequence.getName());
Object obj = null;
- if (av.alignment.isNucleotide())
+ if (av.getAlignment().isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ "");
@@ -713,7 +733,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
ap.alignFrame.statusBar.setText(text.toString());
StringBuffer tooltipText = new StringBuffer();
- SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
if (groups != null)
{
for (int g = 0; g < groups.length; g++)
@@ -912,14 +932,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
- SequenceI seq = av.alignment.getSequenceAt(startseq);
+ SequenceI seq = av.getAlignment().getSequenceAt(startseq);
- if (!groupEditing && av.hasHiddenRows)
+ if (!groupEditing && av.hasHiddenRows())
{
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.isHiddenRepSequence(seq))
{
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ sg = (SequenceGroup) av.getRepresentedSequences(seq);
groupEditing = true;
}
}
@@ -927,15 +946,15 @@ public class SeqPanel extends Panel implements MouseMotionListener,
StringBuffer message = new StringBuffer();
if (groupEditing)
{
- message.append("Edit group:");
+ message.append(MessageManager.getString("action.edit_group")).append(":");
if (editCommand == null)
{
- editCommand = new EditCommand("Edit Group");
+ editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
}
}
else
{
- message.append("Edit sequence: " + seq.getName());
+ message.append(MessageManager.getString("label.edit_sequence")).append(" " + seq.getName());
String label = seq.getName();
if (label.length() > 10)
{
@@ -943,7 +962,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
}
}
@@ -961,7 +980,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// Are we editing within a selection group?
if (groupEditing
- || (sg != null && sg.getSequences(av.hiddenRepSequences)
+ || (sg != null && sg.getSequences(av.getHiddenRepSequences())
.contains(seq)))
{
fixedColumns = true;
@@ -970,14 +989,13 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// but the sequence represents a group
if (sg == null)
{
- if (av.hiddenRepSequences == null
- || !av.hiddenRepSequences.containsKey(seq))
+ if (!av.isHiddenRepSequence(seq))
{
endEditing();
return;
}
- sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ sg = av.getRepresentedSequences(seq);
}
fixedLeft = sg.getStartRes();
@@ -1004,7 +1022,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
fixedColumns = true;
int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
@@ -1034,13 +1052,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
if (groupEditing)
{
- Vector vseqs = sg.getSequences(av.hiddenRepSequences);
- int g, groupSize = vseqs.size();
- SequenceI[] groupSeqs = new SequenceI[groupSize];
- for (g = 0; g < groupSeqs.length; g++)
- {
- groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
- }
+ SequenceI[] groupSeqs = sg.getSequences(av.getHiddenRepSequences())
+ .toArray(new SequenceI[0]);
// drag to right
if (insertGap)
@@ -1048,9 +1061,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// If the user has selected the whole sequence, and is dragging to
// the right, we can still extend the alignment and selectionGroup
if (sg.getStartRes() == 0 && sg.getEndRes() == fixedRight
- && sg.getEndRes() == av.alignment.getWidth() - 1)
+ && sg.getEndRes() == av.getAlignment().getWidth() - 1)
{
- sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+ sg.setEndRes(av.getAlignment().getWidth() + startres - lastres);
fixedRight = sg.getEndRes();
}
@@ -1062,12 +1075,12 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
blank = true;
- for (g = 0; g < groupSize; g++)
+ for (SequenceI gs : groupSeqs)
{
for (int j = 0; j < startres - lastres; j++)
{
- if (!jalview.util.Comparison.isGap(groupSeqs[g]
- .getCharAt(fixedRight - j)))
+ if (!jalview.util.Comparison.isGap(gs.getCharAt(fixedRight
+ - j)))
{
blank = false;
break;
@@ -1082,19 +1095,20 @@ public class SeqPanel extends Panel implements MouseMotionListener,
if (!blank)
{
- if (sg.getSize() == av.alignment.getHeight())
+ if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns && startres < av.getColumnSelection()
- .getHiddenBoundaryRight(startres)))
+ if ((av.hasHiddenColumns() && startres < av
+ .getColumnSelection().getHiddenBoundaryRight(startres)))
{
endEditing();
return;
}
- int alWidth = av.alignment.getWidth();
- if (av.hasHiddenRows)
+ int alWidth = av.getAlignment().getWidth();
+ if (av.hasHiddenRows())
{
- int hwidth = av.alignment.getHiddenSequences().getWidth();
+ int hwidth = av.getAlignment().getHiddenSequences()
+ .getWidth();
if (hwidth > alWidth)
{
alWidth = hwidth;
@@ -1119,16 +1133,16 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// / Are we able to delete?
// ie are all columns blank?
- for (g = 0; g < groupSize; g++)
+ for (SequenceI gs : groupSeqs)
{
for (int j = startres; j < lastres; j++)
{
- if (groupSeqs[g].getLength() <= j)
+ if (gs.getLength() <= j)
{
continue;
}
- if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+ if (!jalview.util.Comparison.isGap(gs.getCharAt(j)))
{
// Not a gap, block edit not valid
endEditing();
@@ -1151,7 +1165,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
else
{
editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
- startres, startres - lastres, av.alignment, true);
+ startres, startres - lastres, av.getAlignment(), true);
}
}
else
@@ -1167,7 +1181,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
else
{
editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
- startres, lastres - startres, av.alignment, true);
+ startres, lastres - startres, av.getAlignment(), true);
}
}
@@ -1189,7 +1203,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
else
{
editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres, av.alignment, true);
+ { seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
else
@@ -1224,7 +1238,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
if (max > 0)
{
editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
- { seq }, startres, max, av.alignment, true);
+ { seq }, startres, max, av.getAlignment(), true);
}
}
}
@@ -1260,21 +1274,21 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
- av.alignment, true);
+ av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
- true);
+ editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1,
+ av.getAlignment(), true);
}
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment,
- true);
+ editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
+ av.getAlignment(), true);
editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
- av.alignment, true);
+ av.getAlignment(), true);
}
// ////////////////////////////////////////
@@ -1309,7 +1323,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
if (stretchGroup == null)
{
- stretchGroup = av.alignment.findGroup(sequence);
+ stretchGroup = av.getAlignment().findGroup(sequence);
if (stretchGroup != null && res > stretchGroup.getStartRes()
&& res < stretchGroup.getEndRes())
{
@@ -1327,7 +1341,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
stretchGroup = null;
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
if (allGroups != null)
{
@@ -1415,28 +1429,17 @@ public class SeqPanel extends Panel implements MouseMotionListener,
return;
}
+ stretchGroup.recalcConservation(); // always do this - annotation has own
+ // state
if (stretchGroup.cs != null)
{
- if (stretchGroup.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
- stretchGroup.getSequences(av.hiddenRepSequences),
- stretchGroup.getWidth());
- }
-
- if (stretchGroup.cs instanceof Blosum62ColourScheme
- || stretchGroup.cs instanceof PIDColourScheme
- || stretchGroup.cs.conservationApplied()
- || stretchGroup.cs.getThreshold() > 0)
- {
- stretchGroup.recalcConservation();
- }
+ stretchGroup.cs.alignmentChanged(stretchGroup,
+ av.getHiddenRepSequences());
if (stretchGroup.cs.conservationApplied())
{
SliderPanel.setConservationSlider(ap, stretchGroup.cs,
stretchGroup.getName());
- stretchGroup.recalcConservation();
}
else
{
@@ -1469,14 +1472,14 @@ public class SeqPanel extends Panel implements MouseMotionListener,
mouseDragging = true;
- if (y > av.alignment.getHeight())
+ if (y > av.getAlignment().getHeight())
{
- y = av.alignment.getHeight() - 1;
+ y = av.getAlignment().getHeight() - 1;
}
- if (res >= av.alignment.getWidth())
+ if (res >= av.getAlignment().getWidth())
{
- res = av.alignment.getWidth() - 1;
+ res = av.getAlignment().getWidth() - 1;
}
if (stretchGroup.getEndRes() == res)
@@ -1521,7 +1524,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
dragDirection = -1;
}
- while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+ while ((y != oldSeq) && (oldSeq > -1)
+ && (y < av.getAlignment().getHeight()))
{
// This routine ensures we don't skip any sequences, as the
// selection is quite slow.
@@ -1658,7 +1662,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
if (mouseDragging && evt.getY() >= getSize().height
- && av.alignment.getHeight() > av.getEndSeq())
+ && av.getAlignment().getHeight() > av.getEndSeq())
{
running = ap.scrollUp(false);
}
@@ -1683,6 +1687,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
}
}
}
+
/**
* modify current selection according to a received message.
*/
@@ -1693,9 +1698,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// handles selection messages...
// TODO: extend config options to allow user to control if selections may be
// shared between viewports.
- if (av!=null && (av == source
- || !av.followSelection
- || (source instanceof AlignViewport && ((AlignViewport) source)
+ if (av != null
+ && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignViewport) source)
.getSequenceSetId().equals(av.getSequenceSetId()))))
{
return;
@@ -1705,20 +1709,22 @@ public class SeqPanel extends Panel implements MouseMotionListener,
// rules are: colsel is copied if there is a real intersection between
// sequence selection
boolean repaint = false, copycolsel = true;
- if (av.selectionGroup == null || !av.isSelectionGroupChanged())
+ if (av.getSelectionGroup() == null || !av.isSelectionGroupChanged(true))
{
SequenceGroup sgroup = null;
- if (seqsel != null)
+ if (seqsel != null && seqsel.getSize() > 0)
{
- if (av.alignment == null)
+ if (av.getAlignment() == null)
{
- System.out.println("Selection message: alignviewport av SeqSetId="
- + av.getSequenceSetId() + " ViewId=" + av.getViewId()
- + " 's alignment is NULL! returning immediatly.");
+ System.out
+ .println("Selection message: alignviewport av SeqSetId="
+ + av.getSequenceSetId() + " ViewId="
+ + av.getViewId()
+ + " 's alignment is NULL! returning immediatly.");
return;
}
- sgroup = seqsel.intersect(av.alignment,
- (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+ sgroup = seqsel.intersect(av.getAlignment(),
+ (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
if ((sgroup == null || sgroup.getSize() == 0)
&& (colsel == null || colsel.size() == 0))
{
@@ -1734,44 +1740,85 @@ public class SeqPanel extends Panel implements MouseMotionListener,
{
av.setSelectionGroup(null);
}
- repaint = av.isSelectionGroupChanged();
+ repaint = av.isSelectionGroupChanged(true);
}
- if (copycolsel && (av.colSel == null || !av.isColSelChanged()))
+ if (copycolsel
+ && (av.getColumnSelection() == null || !av
+ .isColSelChanged(true)))
{
// the current selection is unset or from a previous message
// so import the new colsel.
if (colsel == null || colsel.size() == 0)
{
- if (av.colSel != null)
+ if (av.getColumnSelection() != null)
{
- av.colSel.clear();
+ av.getColumnSelection().clear();
}
}
else
{
// TODO: shift colSel according to the intersecting sequences
- if (av.colSel == null)
+ if (av.getColumnSelection() == null)
{
- av.colSel = new ColumnSelection(colsel);
+ av.setColumnSelection(new ColumnSelection(colsel));
}
else
{
- av.colSel.setElementsFrom(colsel);
+ av.getColumnSelection().setElementsFrom(colsel);
}
}
- repaint |= av.isColSelChanged();
+ repaint |= av.isColSelChanged(true);
}
- if (copycolsel && av.hasHiddenColumns
- && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+ if (copycolsel
+ && av.hasHiddenColumns()
+ && (av.getColumnSelection() == null || av.getColumnSelection()
+ .getHiddenColumns() == null))
{
System.err.println("Bad things");
}
if (repaint)
{
- // probably finessing with multiple redraws here
- PaintRefresher.Refresh(this, av.getSequenceSetId());
- // ap.paintAlignment(false);
+ ap.scalePanelHolder.repaint();
+ ap.repaint();
}
}
+ /**
+ * scroll to the given row/column - or nearest visible location
+ *
+ * @param row
+ * @param column
+ */
+ public void scrollTo(int row, int column)
+ {
+
+ row = row < 0 ? ap.av.startSeq : row;
+ column = column < 0 ? ap.av.startRes : column;
+ ap.scrollTo(column, column, row, true, true);
+ }
+
+ /**
+ * scroll to the given row - or nearest visible location
+ *
+ * @param row
+ */
+ public void scrollToRow(int row)
+ {
+
+ row = row < 0 ? ap.av.startSeq : row;
+ ap.scrollTo(ap.av.startRes, ap.av.startRes, row, true, true);
+ }
+
+ /**
+ * scroll to the given column - or nearest visible location
+ *
+ * @param column
+ */
+ public void scrollToColumn(int column)
+ {
+
+ column = column < 0 ? ap.av.startRes : column;
+ ap.scrollTo(column, column, ap.av.startSeq, true, true);
+ }
+
}