X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=1cc87156c7a93ba356bd31c29d6df1c27f9a0b3b;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=a84d45411edd90367025436d5ab651e7e51dcfcc;hpb=2026a420963f094072607c0495b6369ba96e60c0;p=jalview.git
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index a84d454..1cc8715 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,33 +1,57 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.structure.*;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.SequenceAnnotationReport;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.SequenceListener;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
@@ -87,7 +111,9 @@ public class SeqPanel extends JPanel implements MouseListener,
java.net.URL linkImageURL;
- StringBuffer tooltipText = new StringBuffer("");
+ private final SequenceAnnotationReport seqARep;
+
+ StringBuffer tooltipText = new StringBuffer();
String tmpString;
@@ -106,6 +132,7 @@ public class SeqPanel extends JPanel implements MouseListener,
public SeqPanel(AlignViewport av, AlignmentPanel ap)
{
linkImageURL = getClass().getResource("/images/link.gif");
+ seqARep = new SequenceAnnotationReport(linkImageURL.toString());
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
@@ -123,7 +150,7 @@ public class SeqPanel extends JPanel implements MouseListener,
addMouseMotionListener(this);
addMouseListener(this);
addMouseWheelListener(this);
- ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance);
+ ssm = av.getStructureSelectionManager();
ssm.addStructureViewerListener(this);
ssm.addSelectionListener(this);
}
@@ -168,15 +195,16 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- if (x>seqCanvas.getWidth()+seqCanvas.getWidth())
+ if (x > seqCanvas.getWidth() + seqCanvas.getWidth())
{
- // make sure we calculate relative to visible alignment, rather than right-hand gutter
- x = seqCanvas.getX()+seqCanvas.getWidth();
+ // make sure we calculate relative to visible alignment, rather than
+ // right-hand gutter
+ x = seqCanvas.getX() + seqCanvas.getWidth();
}
res = (x / av.getCharWidth()) + av.getStartRes();
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
@@ -203,54 +231,18 @@ public class SeqPanel extends JPanel implements MouseListener,
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(),
- av.alignment.getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
+ .getHeight() - 1);
}
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);
}
return seq;
}
- SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
- {
- Vector tmp = new Vector();
- SequenceFeature[] features = sequence.getSequenceFeatures();
- if (features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (av.featuresDisplayed == null
- || !av.featuresDisplayed.containsKey(features[i].getType()))
- {
- continue;
- }
-
- if (features[i].featureGroup != null
- && seqCanvas.fr.featureGroups != null
- && seqCanvas.fr.featureGroups
- .containsKey(features[i].featureGroup)
- && !((Boolean) seqCanvas.fr.featureGroups
- .get(features[i].featureGroup)).booleanValue())
- continue;
-
- if ((features[i].getBegin() <= res)
- && (features[i].getEnd() >= res))
- {
- tmp.addElement(features[i]);
- }
- }
- }
-
- features = new SequenceFeature[tmp.size()];
- tmp.copyInto(features);
-
- return features;
- }
-
void endEditing()
{
if (editCommand != null && editCommand.getSize() > 0)
@@ -297,10 +289,9 @@ public class SeqPanel extends JPanel implements MouseListener,
void setCursorPosition()
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
- seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
- seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
scrollToVisible();
}
@@ -308,19 +299,20 @@ public class SeqPanel extends JPanel implements MouseListener,
{
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;
}
@@ -335,18 +327,18 @@ public class SeqPanel extends JPanel implements MouseListener,
{
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();
@@ -366,7 +358,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
if (!av.wrapAlignment)
{
- while (seqCanvas.cursorX < av.colSel
+ while (seqCanvas.cursorX < av.getColumnSelection()
.adjustForHiddenColumns(av.startRes))
{
if (!ap.scrollRight(false))
@@ -374,7 +366,7 @@ public class SeqPanel extends JPanel implements MouseListener,
break;
}
}
- while (seqCanvas.cursorX > av.colSel
+ while (seqCanvas.cursorX > av.getColumnSelection()
.adjustForHiddenColumns(av.endRes))
{
if (!ap.scrollRight(true))
@@ -384,7 +376,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
}
- setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+ setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
seqCanvas.cursorX, seqCanvas.cursorY);
seqCanvas.repaint();
@@ -392,17 +384,16 @@ public class SeqPanel extends JPanel implements MouseListener,
void setSelectionAreaAtCursor(boolean topLeft)
{
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
- seqCanvas.cursorY);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
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;
@@ -447,7 +438,7 @@ public class SeqPanel extends JPanel implements MouseListener,
sg.getSequences(null).clear();
for (int i = min; i < max; i++)
{
- sg.addSequence(av.alignment.getSequenceAt(i), false);
+ sg.addSequence(av.getAlignment().getSequenceAt(i), false);
}
}
}
@@ -482,13 +473,14 @@ public class SeqPanel extends JPanel implements MouseListener,
editSequence(false, false, seqCanvas.cursorX);
endEditing();
}
-
- void insertNucAtCursor(boolean group,String nuc){
- groupEditing = group;
- startseq = seqCanvas.cursorY;
- lastres = seqCanvas.cursorX;
- editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
- endEditing();
+
+ void insertNucAtCursor(boolean group, String nuc)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
+ endEditing();
}
void numberPressed(char value)
@@ -510,26 +502,36 @@ public class SeqPanel extends JPanel implements MouseListener,
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;
}
/**
@@ -538,6 +540,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseReleased(MouseEvent evt)
{
mouseDragging = false;
@@ -558,6 +561,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mousePressed(MouseEvent evt)
{
lastMousePress = evt.getPoint();
@@ -607,6 +611,7 @@ public class SeqPanel extends JPanel implements MouseListener,
String lastMessage;
+ @Override
public void mouseOverSequence(SequenceI sequence, int index, int pos)
{
String tmp = sequence.hashCode() + " " + index + " " + pos;
@@ -619,18 +624,20 @@ public class SeqPanel extends JPanel implements MouseListener,
lastMessage = tmp;
}
+ @Override
public void highlightSequence(SearchResults results)
{
if (av.followHighlight)
{
if (ap.scrollToPosition(results, false))
{
- seqCanvas.revalidate();
+ seqCanvas.revalidate();
}
}
seqCanvas.highlightSearchResults(results);
}
+ @Override
public void updateColours(SequenceI seq, int index)
{
System.out.println("update the seqPanel colours");
@@ -643,6 +650,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseMoved(MouseEvent evt)
{
if (editingSeqs)
@@ -669,22 +677,19 @@ public class SeqPanel extends JPanel implements MouseListener,
pos = setStatusMessage(sequence, res, seq);
if (ssm != null && pos > -1)
+ {
mouseOverSequence(sequence, res, pos);
+ }
tooltipText.setLength(6); // Cuts the buffer back to
- SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
if (groups != null)
{
for (int g = 0; g < groups.length; g++)
{
if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
{
- if (tooltipText.length() > 6)
- {
- tooltipText.append("
");
- }
-
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
{
@@ -700,14 +705,14 @@ public class SeqPanel extends JPanel implements MouseListener,
}
// use aa to see if the mouse pointer is on a
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
int rpos;
- SequenceFeature[] features = findFeaturesAtRes(
+ List features = ap.getFeatureRenderer().findFeaturesAtRes(
sequence.getDatasetSequence(),
rpos = sequence.findPosition(res));
- appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
- this.ap.seqPanel.seqCanvas.fr.minmax);
+ seqARep.appendFeatures(tooltipText, rpos, features,
+ this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
if (tooltipText.length() == 6) //
{
@@ -716,11 +721,13 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- tooltipText.append("");
if (lastTooltip == null
|| !lastTooltip.equals(tooltipText.toString()))
{
- setToolTipText(tooltipText.toString());
+ String formatedTooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltipText.toString());
+ // String formatedTooltipText = tooltipText.toString();
+ setToolTipText(formatedTooltipText);
lastTooltip = tooltipText.toString();
}
@@ -752,146 +759,6 @@ public class SeqPanel extends JPanel implements MouseListener,
return lastp = p;
}
- /**
- * appends the features at rpos to the given stringbuffer ready for display in
- * a tooltip
- *
- * @param tooltipText2
- * @param linkImageURL
- * @param rpos
- * @param features
- * TODO refactor to Jalview 'utilities' somehow.
- */
- public void appendFeatures(StringBuffer tooltipText2,
- String linkImageURL, int rpos, SequenceFeature[] features)
- {
- appendFeatures(tooltipText2, linkImageURL, rpos, features, null);
- }
-
- public void appendFeatures(StringBuffer tooltipText2, String string,
- int rpos, SequenceFeature[] features, Hashtable minmax)
- {
- String tmpString;
- if (features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (features[i].getType().equals("disulfide bond"))
- {
- if (features[i].getBegin() == rpos
- || features[i].getEnd() == rpos)
- {
- if (tooltipText2.length() > 6)
- {
- tooltipText2.append("
");
- }
- tooltipText2.append("disulfide bond " + features[i].getBegin()
- + ":" + features[i].getEnd());
- if (features[i].links != null)
- {
- tooltipText2.append(" ![](\"")
");
- }
- }
- }
- else
- {
- if (tooltipText2.length() > 6)
- {
- tooltipText2.append("
");
- }
- // TODO: remove this hack to display link only features
- boolean linkOnly = features[i].getValue("linkonly") != null;
- if (!linkOnly)
- {
- tooltipText2.append(features[i].getType() + " ");
- if (rpos != 0)
- {
- // we are marking a positional feature
- tooltipText2.append(features[i].begin);
- }
- if (features[i].begin != features[i].end)
- {
- tooltipText2.append(" " + features[i].end);
- }
-
- if (features[i].getDescription() != null
- && !features[i].description.equals(features[i]
- .getType()))
- {
- tmpString = features[i].getDescription();
- String tmp2up=tmpString.toUpperCase();
- int startTag = tmp2up.indexOf("");
- if (startTag > -1)
- {
- tmpString = tmpString.substring(startTag + 6);
- tmp2up = tmp2up.substring(startTag+6);
- }
- int endTag = tmp2up.indexOf("");
- if (endTag > -1)
- {
- tmpString = tmpString.substring(0, endTag);
- tmp2up = tmp2up.substring(0, endTag);
- }
- endTag = tmp2up.indexOf("");
- if (endTag > -1)
- {
- tmpString = tmpString.substring(0, endTag);
- }
-
- if (startTag > -1)
- {
- tooltipText2.append("; " + tmpString);
- }
- else
- {
- if (tmpString.indexOf("<") > -1
- || tmpString.indexOf(">") > -1)
- {
- // The description does not specify html is to
- // be used, so we must remove < > symbols
- tmpString = tmpString.replaceAll("<", "<");
- tmpString = tmpString.replaceAll(">", ">");
-
- tooltipText2.append("; ");
- tooltipText2.append(tmpString);
-
- }
- else
- {
- tooltipText2.append("; " + tmpString);
- }
- }
- }
- // check score should be shown
- if (features[i].getScore() != Float.NaN)
- {
- float[][] rng = (minmax == null) ? null : ((float[][]) minmax
- .get(features[i].getType()));
- if (rng != null && rng[0] != null && rng[0][0] != rng[0][1])
- {
- tooltipText2.append(" Score=" + features[i].getScore());
- }
- }
- if (features[i].getValue("status") != null)
- {
- String status = features[i].getValue("status").toString();
- if (status.length() > 0)
- {
- tooltipText2.append("; (" + features[i].getValue("status")
- + ")");
- }
- }
- }
- if (features[i].links != null)
- {
- tooltipText2.append(" ");
- }
-
- }
- }
- }
- }
-
String lastTooltip;
/**
@@ -912,7 +779,7 @@ public class SeqPanel extends JPanel implements MouseListener,
+ sequence.getName());
Object obj = null;
- if (av.alignment.isNucleotide())
+ if (av.getAlignment().isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res)
+ "");
@@ -948,6 +815,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (mouseWheelPressed)
@@ -1021,11 +889,11 @@ public class SeqPanel extends JPanel implements MouseListener,
if ((res < av.getAlignment().getWidth()) && (res < lastres))
{
// dragLeft, delete gap
- editSequence(false, false,res);
+ editSequence(false, false, res);
}
else
{
- editSequence(true, false,res);
+ editSequence(true, false, res);
}
mouseDragging = true;
@@ -1035,23 +903,23 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
- //TODO: Make it more clever than many booleans
- synchronized void editSequence(boolean insertGap, boolean editSeq, int startres)
+ // TODO: Make it more clever than many booleans
+ synchronized void editSequence(boolean insertGap, boolean editSeq,
+ int startres)
{
int fixedLeft = -1;
int fixedRight = -1;
boolean fixedColumns = false;
SequenceGroup sg = av.getSelectionGroup();
- SequenceI seq = av.alignment.getSequenceAt(startseq);
+ SequenceI seq = av.getAlignment().getSequenceAt(startseq);
// No group, but the sequence may represent a group
- 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 = av.getRepresentedSequences(seq);
groupEditing = true;
}
}
@@ -1062,7 +930,7 @@ public class SeqPanel extends JPanel implements MouseListener,
message.append("Edit group:");
if (editCommand == null)
{
- editCommand = new EditCommand("Edit Group");
+ editCommand = new EditCommand(MessageManager.getString("action.edit_group"));
}
}
else
@@ -1075,7 +943,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
if (editCommand == null)
{
- editCommand = new EditCommand("Edit " + label);
+ editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label}));
}
}
@@ -1093,7 +961,7 @@ public class SeqPanel extends JPanel implements MouseListener,
// 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;
@@ -1102,13 +970,12 @@ public class SeqPanel extends JPanel implements MouseListener,
// 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();
@@ -1135,7 +1002,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
fixedColumns = true;
int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
@@ -1165,12 +1032,12 @@ public class SeqPanel extends JPanel implements MouseListener,
if (groupEditing)
{
- Vector vseqs = sg.getSequences(av.hiddenRepSequences);
+ List vseqs = sg.getSequences(av.getHiddenRepSequences());
int g, groupSize = vseqs.size();
SequenceI[] groupSeqs = new SequenceI[groupSize];
for (g = 0; g < groupSeqs.length; g++)
{
- groupSeqs[g] = (SequenceI) vseqs.elementAt(g);
+ groupSeqs[g] = vseqs.get(g);
}
// drag to right
@@ -1179,9 +1046,9 @@ public class SeqPanel extends JPanel implements MouseListener,
// 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();
}
@@ -1213,19 +1080,20 @@ public class SeqPanel extends JPanel implements MouseListener,
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;
@@ -1281,8 +1149,8 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
- startres, startres - lastres, av.alignment, true);
+ editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
+ startres, startres - lastres, av.getAlignment(), true);
}
}
else
@@ -1297,8 +1165,8 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
- startres, lastres - startres, av.alignment, true);
+ editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
+ startres, lastres - startres, av.getAlignment(), true);
}
}
@@ -1319,61 +1187,65 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
- { seq }, lastres, startres - lastres, av.alignment, true);
- }
+ editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
+ { seq }, lastres, startres - lastres, av.getAlignment(), true);
+ }
}
else
{
- if(!editSeq){
- // dragging to the left
- if (fixedColumns && fixedRight != -1)
+ if (!editSeq)
{
- for (int j = lastres; j > startres; j--)
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+ for (int j = lastres; j > startres; j--)
{
- endEditing();
- break;
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
+ {
+ endEditing();
+ break;
+ }
+ deleteChar(startres, new SequenceI[]
+ { seq }, fixedRight);
+ }
+ }
+ else
+ {
+ // could be a keyboard edit trying to delete none gaps
+ int max = 0;
+ for (int m = startres; m < lastres; m++)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+ {
+ break;
+ }
+ max++;
+ }
+
+ if (max > 0)
+ {
+ editCommand.appendEdit(Action.DELETE_GAP,
+ new SequenceI[]
+ { seq }, startres, max, av.getAlignment(), true);
}
- deleteChar(startres, new SequenceI[]
- { seq }, fixedRight);
}
}
else
- {
- // could be a keyboard edit trying to delete none gaps
- int max = 0;
- for (int m = startres; m < lastres; m++)
+ {// insertGap==false AND editSeq==TRUE;
+ if (fixedColumns && fixedRight != -1)
{
- if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+ for (int j = lastres; j < startres; j++)
{
- break;
+ insertChar(j, new SequenceI[]
+ { seq }, fixedRight);
}
- max++;
}
-
- if (max > 0)
+ else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
- { seq }, startres, max, av.alignment, true);
+ editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[]
+ { seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
- }else{//insertGap==false AND editSeq==TRUE;
- if (fixedColumns && fixedRight != -1)
- {
- for (int j = lastres; j < startres; j++)
- {
- insertChar(j, new SequenceI[]
- { seq }, fixedRight);
- }
- }
- else
- {
- editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
- { seq }, lastres, startres - lastres, av.alignment, true);
- }
- }
}
}
@@ -1406,22 +1278,22 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
- av.alignment, true);
+ editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
+ av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment,
- true);
+ editCommand.appendEdit(Action.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(Action.DELETE_GAP, seq, j, 1,
+ av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
- av.alignment, true);
+ editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
+ av.getAlignment(), true);
}
/**
@@ -1430,6 +1302,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mouseEntered(MouseEvent e)
{
if (oldSeq < 0)
@@ -1450,6 +1323,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
@@ -1463,10 +1337,11 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
SequenceGroup sg = null;
- SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+ SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
if (evt.getClickCount() > 1)
{
sg = av.getSelectionGroup();
@@ -1476,37 +1351,53 @@ public class SeqPanel extends JPanel implements MouseListener,
av.setSelectionGroup(null);
}
- SequenceFeature[] features = findFeaturesAtRes(
+ List features = seqCanvas.getFeatureRenderer().findFeaturesAtRes(
sequence.getDatasetSequence(),
sequence.findPosition(findRes(evt)));
- if (features != null && features.length > 0)
+ if (features != null && features.size()> 0)
{
SearchResults highlight = new SearchResults();
- highlight.addResult(sequence, features[0].getBegin(),
- features[0].getEnd());
+ highlight.addResult(sequence, features.get(0).getBegin(),
+ features.get(0).getEnd());
seqCanvas.highlightSearchResults(highlight);
}
- if (features != null && features.length > 0)
+ if (features != null && features.size()> 0)
{
seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[]
- { sequence }, features, false, ap);
+ { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap);
seqCanvas.highlightSearchResults(null);
}
}
}
+ @Override
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
if (e.getWheelRotation() > 0)
{
- ap.scrollUp(false);
+ if (e.isShiftDown())
+ {
+ ap.scrollRight(true);
+
+ }
+ else
+ {
+ ap.scrollUp(false);
+ }
}
else
{
- ap.scrollUp(true);
+ if (e.isShiftDown())
+ {
+ ap.scrollRight(false);
+ }
+ else
+ {
+ ap.scrollUp(true);
+ }
}
// TODO Update tooltip for new position.
}
@@ -1525,11 +1416,12 @@ public class SeqPanel extends JPanel implements MouseListener,
startWrapBlock = wrappedBlock;
- if (av.wrapAlignment && seq > av.alignment.getHeight())
+ if (av.wrapAlignment && seq > av.getAlignment().getHeight())
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Cannot edit annotations in wrapped view.",
- "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("label.cannot_edit_annotations_in_wrapped_view"),
+ MessageManager.getString("label.wrapped_view_no_edit"),
+ JOptionPane.WARNING_MESSAGE);
return;
}
@@ -1538,7 +1430,7 @@ public class SeqPanel extends JPanel implements MouseListener,
return;
}
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
if ((sequence == null) || (res > sequence.getLength()))
{
@@ -1549,7 +1441,7 @@ public class SeqPanel extends JPanel implements MouseListener,
if (stretchGroup == null)
{
- stretchGroup = av.alignment.findGroup(sequence);
+ stretchGroup = av.getAlignment().findGroup(sequence);
if ((stretchGroup != null) && (res > stretchGroup.getStartRes())
&& (res < stretchGroup.getEndRes()))
@@ -1567,7 +1459,7 @@ public class SeqPanel extends JPanel implements MouseListener,
{
stretchGroup = null;
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+ SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence);
if (allGroups != null)
{
@@ -1588,16 +1480,16 @@ public class SeqPanel extends JPanel implements MouseListener,
if (javax.swing.SwingUtilities.isRightMouseButton(evt))
{
- SequenceFeature[] allFeatures = findFeaturesAtRes(
+ List allFeatures = ap.getFeatureRenderer().findFeaturesAtRes(
sequence.getDatasetSequence(), sequence.findPosition(res));
Vector links = new Vector();
- for (int i = 0; i < allFeatures.length; i++)
+ for (SequenceFeature sf:allFeatures)
{
- if (allFeatures[i].links != null)
+ if (sf.links != null)
{
- for (int j = 0; j < allFeatures[i].links.size(); j++)
+ for (int j = 0; j < sf.links.size(); j++)
{
- links.addElement(allFeatures[i].links.elementAt(j));
+ links.addElement(sf.links.elementAt(j));
}
}
}
@@ -1673,12 +1565,8 @@ public class SeqPanel extends JPanel implements MouseListener,
// state
if (stretchGroup.cs != null)
{
- if (stretchGroup.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(
- stretchGroup.getSequences(av.hiddenRepSequences),
- stretchGroup.getWidth());
- }
+ stretchGroup.cs.alignmentChanged(stretchGroup,
+ av.getHiddenRepSequences());
if (stretchGroup.cs.conservationApplied())
{
@@ -1721,9 +1609,9 @@ public class SeqPanel extends JPanel implements MouseListener,
return;
}
- if (res >= av.alignment.getWidth())
+ if (res >= av.getAlignment().getWidth())
{
- res = av.alignment.getWidth() - 1;
+ res = av.getAlignment().getWidth() - 1;
}
if (stretchGroup.getEndRes() == res)
@@ -1768,7 +1656,8 @@ public class SeqPanel extends JPanel implements MouseListener,
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.
@@ -1859,6 +1748,7 @@ public class SeqPanel extends JPanel implements MouseListener,
running = false;
}
+ @Override
public void run()
{
running = true;
@@ -1873,7 +1763,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
if (mouseDragging && (evt.getY() >= getHeight())
- && (av.alignment.getHeight() > av.getEndSeq()))
+ && (av.getAlignment().getHeight() > av.getEndSeq()))
{
running = ap.scrollUp(false);
}
@@ -1901,6 +1791,7 @@ public class SeqPanel extends JPanel implements MouseListener,
/**
* modify current selection according to a received message.
*/
+ @Override
public void selection(SequenceGroup seqsel, ColumnSelection colsel,
SelectionSource source)
{
@@ -1910,7 +1801,8 @@ public class SeqPanel extends JPanel implements MouseListener,
// shared between viewports.
if (av == source
|| !av.followSelection
- || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+ || (av.isSelectionGroupChanged(false) || av
+ .isColSelChanged(false))
|| (source instanceof AlignViewport && ((AlignViewport) source)
.getSequenceSetId().equals(av.getSequenceSetId())))
{
@@ -1924,17 +1816,17 @@ public class SeqPanel extends JPanel implements MouseListener,
// if (!av.isSelectionGroupChanged(false))
{
SequenceGroup sgroup = null;
- if (seqsel != null && seqsel.getSize()>0)
+ if (seqsel != null && seqsel.getSize() > 0)
{
- if (av.alignment == null)
+ if (av.getAlignment() == null)
{
jalview.bin.Cache.log.warn("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))
{
@@ -1959,29 +1851,31 @@ public class SeqPanel extends JPanel implements MouseListener,
// so import the new colsel.
if (colsel == null || colsel.size() == 0)
{
- if (av.colSel != null)
+ if (av.getColumnSelection() != null)
{
- av.colSel.clear();
- repaint=true;
+ av.getColumnSelection().clear();
+ repaint = true;
}
}
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);
}
}
av.isColSelChanged(true);
repaint = 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");
}