X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=7c6a202577e1ca023a321f00c6a5d40b1994f3f5;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=9c3d557af1c9ee6dea0ae5e7a7cc9d47aa4e737a;hpb=fc853e3c385e32591ceac07070d37932fcf87941;p=jalview.git
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 9c3d557..7c6a202 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,36 +1,57 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.gui;
-import java.util.*;
+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 java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.SequenceAnnotationReport;
-import jalview.schemes.*;
-import jalview.structure.*;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
/**
* DOCUMENT ME!
@@ -92,7 +113,7 @@ public class SeqPanel extends JPanel implements MouseListener,
private final SequenceAnnotationReport seqARep;
- StringBuffer tooltipText = new StringBuffer("");
+ StringBuffer tooltipText = new StringBuffer();
String tmpString;
@@ -129,8 +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);
}
@@ -223,42 +243,6 @@ public class SeqPanel extends JPanel implements MouseListener,
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)
@@ -307,7 +291,7 @@ public class SeqPanel extends JPanel implements MouseListener,
{
SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
- seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1);
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
scrollToVisible();
}
@@ -518,29 +502,34 @@ public class SeqPanel extends JPanel implements MouseListener,
int getKeyboardNo1()
{
- try {
- if (keyboardNo1 != null)
+ try
{
- int value = Integer.parseInt(keyboardNo1.toString());
- keyboardNo1 = null;
- return value;
- }
+ if (keyboardNo1 != null)
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
} catch (Exception x)
- {}
+ {
+ }
keyboardNo1 = null;
return 1;
}
int getKeyboardNo2()
{
- try {
- if (keyboardNo2!=null){
- int value = Integer.parseInt(keyboardNo2.toString());
- keyboardNo2 = null;
- return value;
- }
+ try
+ {
+ if (keyboardNo2 != null)
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
} catch (Exception x)
- {}
+ {
+ }
keyboardNo2 = null;
return 1;
}
@@ -688,7 +677,9 @@ 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
@@ -699,11 +690,6 @@ public class SeqPanel extends JPanel implements MouseListener,
{
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"))
{
@@ -719,14 +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));
seqARep.appendFeatures(tooltipText, rpos, features,
- this.ap.seqPanel.seqCanvas.fr.minmax);
+ this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
if (tooltipText.length() == 6) //
{
@@ -735,11 +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();
}
@@ -942,7 +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
@@ -955,7 +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}));
}
}
@@ -1161,7 +1149,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+ editCommand.appendEdit(Action.INSERT_GAP, groupSeqs,
startres, startres - lastres, av.getAlignment(), true);
}
}
@@ -1177,7 +1165,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+ editCommand.appendEdit(Action.DELETE_GAP, groupSeqs,
startres, lastres - startres, av.getAlignment(), true);
}
@@ -1199,7 +1187,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[]
+ editCommand.appendEdit(Action.INSERT_GAP, new SequenceI[]
{ seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
@@ -1236,7 +1224,7 @@ public class SeqPanel extends JPanel implements MouseListener,
if (max > 0)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP,
+ editCommand.appendEdit(Action.DELETE_GAP,
new SequenceI[]
{ seq }, startres, max, av.getAlignment(), true);
}
@@ -1254,7 +1242,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
else
{
- editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[]
+ editCommand.appendEdit(Action.INSERT_NUC, new SequenceI[]
{ seq }, lastres, startres - lastres, av.getAlignment(), true);
}
}
@@ -1290,10 +1278,10 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
+ editCommand.appendEdit(Action.DELETE_GAP, seq, blankColumn, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1,
+ editCommand.appendEdit(Action.INSERT_GAP, seq, j, 1,
av.getAlignment(), true);
}
@@ -1301,10 +1289,10 @@ public class SeqPanel extends JPanel implements MouseListener,
void deleteChar(int j, SequenceI[] seq, int fixedColumn)
{
- editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
+ editCommand.appendEdit(Action.DELETE_GAP, seq, j, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
+ editCommand.appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1,
av.getAlignment(), true);
}
@@ -1363,21 +1351,21 @@ 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);
}
@@ -1430,9 +1418,10 @@ public class SeqPanel extends JPanel implements MouseListener,
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;
}
@@ -1491,16 +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));
}
}
}