X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=904b856bc8ff9439e78e1982e377954e2e089cfb;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=13527d05d795dd9108d0a3011ae5f2bce4246483;hpb=b81d4d7d46ea8b1c89df086fb847baab6b69d427;p=jalview.git
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 13527d0..904b856 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,19 +1,20 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * 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.
- *
+ *
* 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
@@ -27,8 +28,10 @@ import javax.swing.*;
import jalview.commands.*;
import jalview.datamodel.*;
+import jalview.io.SequenceAnnotationReport;
import jalview.schemes.*;
import jalview.structure.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
@@ -88,6 +91,8 @@ public class SeqPanel extends JPanel implements MouseListener,
java.net.URL linkImageURL;
+ private final SequenceAnnotationReport seqARep;
+
StringBuffer tooltipText = new StringBuffer("");
String tmpString;
@@ -107,6 +112,7 @@ 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);
@@ -124,7 +130,7 @@ 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);
}
@@ -169,10 +175,11 @@ 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();
}
@@ -204,13 +211,13 @@ public class SeqPanel extends JPanel implements MouseListener,
y -= hgap;
- seq = Math.min((y % cHeight) / av.getCharHeight(),
- av.getAlignment().getHeight() - 1);
+ seq = Math.min((y % cHeight) / av.getCharHeight(), av.getAlignment()
+ .getHeight() - 1);
}
else
{
- seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
- av.getAlignment().getHeight() - 1);
+ seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av
+ .getAlignment().getHeight() - 1);
}
return seq;
@@ -298,10 +305,9 @@ 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();
}
@@ -309,7 +315,8 @@ public class SeqPanel extends JPanel implements MouseListener,
{
seqCanvas.cursorX += dx;
seqCanvas.cursorY += dy;
- if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
+ if (av.hasHiddenColumns()
+ && !av.getColumnSelection().isVisible(seqCanvas.cursorX))
{
int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
@@ -393,8 +400,7 @@ 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)
{
@@ -483,13 +489,14 @@ 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)
@@ -511,26 +518,31 @@ 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)
+ {}
+ 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)
+ {}
+ keyboardNo2 = null;
+ return 1;
}
/**
@@ -539,6 +551,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseReleased(MouseEvent evt)
{
mouseDragging = false;
@@ -559,6 +572,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mousePressed(MouseEvent evt)
{
lastMousePress = evt.getPoint();
@@ -608,6 +622,7 @@ 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;
@@ -620,18 +635,20 @@ 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");
@@ -644,6 +661,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseMoved(MouseEvent evt)
{
if (editingSeqs)
@@ -707,7 +725,7 @@ public class SeqPanel extends JPanel implements MouseListener,
SequenceFeature[] features = findFeaturesAtRes(
sequence.getDatasetSequence(),
rpos = sequence.findPosition(res));
- appendFeatures(tooltipText, linkImageURL.toString(), rpos, features,
+ seqARep.appendFeatures(tooltipText, rpos, features,
this.ap.seqPanel.seqCanvas.fr.minmax);
}
if (tooltipText.length() == 6) //
@@ -753,146 +771,6 @@ 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;
/**
@@ -949,6 +827,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param evt
* DOCUMENT ME!
*/
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (mouseWheelPressed)
@@ -1022,11 +901,11 @@ 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;
@@ -1036,8 +915,9 @@ 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;
@@ -1169,7 +1049,7 @@ public class SeqPanel extends JPanel implements MouseListener,
SequenceI[] groupSeqs = new SequenceI[groupSize];
for (g = 0; g < groupSeqs.length; g++)
{
- groupSeqs[g] = (SequenceI) vseqs.get(g);
+ groupSeqs[g] = vseqs.get(g);
}
// drag to right
@@ -1214,8 +1094,8 @@ public class SeqPanel extends JPanel implements MouseListener,
{
if (sg.getSize() == av.getAlignment().getHeight())
{
- if ((av.hasHiddenColumns() && startres < av.getColumnSelection()
- .getHiddenBoundaryRight(startres)))
+ if ((av.hasHiddenColumns() && startres < av
+ .getColumnSelection().getHiddenBoundaryRight(startres)))
{
endEditing();
return;
@@ -1224,7 +1104,8 @@ public class SeqPanel extends JPanel implements MouseListener,
int alWidth = av.getAlignment().getWidth();
if (av.hasHiddenRows())
{
- int hwidth = av.getAlignment().getHiddenSequences().getWidth();
+ int hwidth = av.getAlignment().getHiddenSequences()
+ .getWidth();
if (hwidth > alWidth)
{
alWidth = hwidth;
@@ -1320,59 +1201,63 @@ public class SeqPanel extends JPanel implements MouseListener,
{
editCommand.appendEdit(EditCommand.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(EditCommand.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.getAlignment(), true);
+ editCommand.appendEdit(EditCommand.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.getAlignment(), true);
- }
- }
}
}
@@ -1408,16 +1293,16 @@ public class SeqPanel extends JPanel implements MouseListener,
editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1,
av.getAlignment(), true);
- editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(),
- 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.getAlignment(),
- true);
+ editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1,
+ av.getAlignment(), true);
editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1,
av.getAlignment(), true);
@@ -1429,6 +1314,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mouseEntered(MouseEvent e)
{
if (oldSeq < 0)
@@ -1449,6 +1335,7 @@ public class SeqPanel extends JPanel implements MouseListener,
* @param e
* DOCUMENT ME!
*/
+ @Override
public void mouseExited(MouseEvent e)
{
if (av.getWrapAlignment())
@@ -1462,6 +1349,7 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
SequenceGroup sg = null;
@@ -1496,16 +1384,32 @@ public class SeqPanel extends JPanel implements MouseListener,
}
}
+ @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.
}
@@ -1527,8 +1431,8 @@ 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);
+ MessageManager.getString("label.cannot_edit_annotations_in_wrapped_view"),
+ MessageManager.getString("label.wrapped_view_no_edit"), JOptionPane.WARNING_MESSAGE);
return;
}
@@ -1537,7 +1441,7 @@ 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()))
{
@@ -1672,11 +1576,8 @@ public class SeqPanel extends JPanel implements MouseListener,
// state
if (stretchGroup.cs != null)
{
- if (stretchGroup.cs instanceof ClustalxColourScheme)
- {
- ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged(
- stretchGroup,av.getHiddenRepSequences());
- }
+ stretchGroup.cs.alignmentChanged(stretchGroup,
+ av.getHiddenRepSequences());
if (stretchGroup.cs.conservationApplied())
{
@@ -1766,7 +1667,8 @@ public class SeqPanel extends JPanel implements MouseListener,
dragDirection = -1;
}
- while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().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.
@@ -1857,6 +1759,7 @@ public class SeqPanel extends JPanel implements MouseListener,
running = false;
}
+ @Override
public void run()
{
running = true;
@@ -1899,6 +1802,7 @@ 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)
{
@@ -1908,7 +1812,8 @@ 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())))
{
@@ -1922,7 +1827,7 @@ 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.getAlignment() == null)
{
@@ -1960,7 +1865,7 @@ public class SeqPanel extends JPanel implements MouseListener,
if (av.getColumnSelection() != null)
{
av.getColumnSelection().clear();
- repaint=true;
+ repaint = true;
}
}
else
@@ -1978,8 +1883,10 @@ public class SeqPanel extends JPanel implements MouseListener,
av.isColSelChanged(true);
repaint = true;
}
- if (copycolsel && av.hasHiddenColumns()
- && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null))
+ if (copycolsel
+ && av.hasHiddenColumns()
+ && (av.getColumnSelection() == null || av.getColumnSelection()
+ .getHiddenColumns() == null))
{
System.err.println("Bad things");
}