X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=a20165a78123a2ffbe1ba0d85225a08d37e50f95;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=a68b226764b068fe899615b961f88783ae5e6389;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index a68b226..a20165a 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -1,6 +1,6 @@
/*
* Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
@@ -18,17 +18,15 @@
*/
package jalview.gui;
-import jalview.datamodel.*;
-
-import jalview.schemes.*;
+import java.util.*;
import java.awt.*;
import java.awt.event.*;
-
-import java.util.*;
-
import javax.swing.*;
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
/**
* DOCUMENT ME!
@@ -36,943 +34,1745 @@ import javax.swing.*;
* @author $author$
* @version $Revision$
*/
-public class SeqPanel extends JPanel
-{
- /** DOCUMENT ME!! */
- public SeqCanvas seqCanvas;
-
- /** DOCUMENT ME!! */
- public AlignmentPanel ap;
- protected int lastres;
- protected int startseq;
- int startEdit = -1;
- int endEdit = -1;
- protected AlignViewport av;
-
- // if character is inserted or deleted, we will need to recalculate the conservation
- int seqEditOccurred = -1;
- ScrollThread scrollThread = null;
- boolean mouseDragging = false;
- boolean editingSeqs = false;
- boolean groupEditing = false;
-
- //////////////////////////////////////////
- /////Everything below this is for defining the boundary of the rubberband
- //////////////////////////////////////////
- int oldSeq = -1;
- boolean changeEndSeq = false;
- boolean changeStartSeq = false;
- boolean changeEndRes = false;
- boolean changeStartRes = false;
- SequenceGroup stretchGroup = null;
- boolean remove = false;
-
- boolean mouseWheelPressed = false;
-
- /**
- * Creates a new SeqPanel object.
- *
- * @param avp DOCUMENT ME!
- * @param p DOCUMENT ME!
- */
- public SeqPanel(AlignViewport avp, AlignmentPanel p)
- {
- ToolTipManager.sharedInstance().registerComponent(this);
- ToolTipManager.sharedInstance().setInitialDelay(0);
- ToolTipManager.sharedInstance().setDismissDelay(10000);
- this.av = avp;
- setBackground(Color.white);
-
- seqCanvas = new SeqCanvas(avp);
- setLayout(new BorderLayout());
- add(seqCanvas, BorderLayout.CENTER);
-
- ap = p;
-
- addMouseMotionListener(new MouseMotionAdapter()
- {
- public void mouseMoved(MouseEvent evt)
- {
- doMouseMoved(evt);
- }
-
- public void mouseDragged(MouseEvent evt)
- {
- if (editingSeqs)
- {
- doMouseDragged(evt);
- }
- else
- {
- doMouseDraggedDefineMode(evt);
- }
- }
- });
-
- addMouseWheelListener(new MouseWheelListener()
- {
- public void mouseWheelMoved(MouseWheelEvent e)
- {
-
- if (mouseWheelPressed)
- {
- Font font = av.getFont();
- int fontSize = font.getSize();
- if (e.getWheelRotation() > 0 && fontSize < 30)
- fontSize++;
- else if (fontSize > 1)
- fontSize--;
-
- av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
- ap.fontChanged();
- }
- else
- {
- if (e.getWheelRotation() > 0)
- ap.scrollUp(false);
- else
- ap.scrollUp(true);
- }
-
- }
- });
-
-
- addMouseListener(new MouseAdapter()
- {
- public void mouseReleased(MouseEvent evt)
- {
- mouseWheelPressed = false;
-
- if (editingSeqs)
- {
- doMouseReleased(evt);
- }
- else
- {
- doMouseReleasedDefineMode(evt);
- }
- }
-
- public void mousePressed(MouseEvent evt)
- {
- if( javax.swing.SwingUtilities.isMiddleMouseButton(evt))
- {
- mouseWheelPressed = true;
- return;
- }
-
- if (evt.isShiftDown() || evt.isAltDown() ||
- evt.isControlDown())
- {
- if (evt.isAltDown() || evt.isControlDown())
- {
- groupEditing = true;
- }
-
- editingSeqs = true;
- doMousePressed(evt);
- }
- else
- {
- doMousePressedDefineMode(evt);
- }
- }
-
- public void mouseExited(MouseEvent evt)
- {
- if (editingSeqs)
- {
- return;
- }
+public class SeqPanel
+ extends JPanel implements MouseListener,
+ MouseMotionListener, MouseWheelListener
- doMouseExitedDefineMode(evt);
- }
-
- public void mouseEntered(MouseEvent evt)
- {
- if (editingSeqs)
- {
- return;
- }
-
- doMouseEnteredDefineMode(evt);
- }
- });
+{
+ /** DOCUMENT ME!! */
+ public SeqCanvas seqCanvas;
+
+ /** DOCUMENT ME!! */
+ public AlignmentPanel ap;
+ protected int lastres;
+ protected int startseq;
+ protected AlignViewport av;
+
+ ScrollThread scrollThread = null;
+ boolean mouseDragging = false;
+ boolean editingSeqs = false;
+ boolean groupEditing = false;
+
+ //////////////////////////////////////////
+ /////Everything below this is for defining the boundary of the rubberband
+ //////////////////////////////////////////
+ int oldSeq = -1;
+ boolean changeEndSeq = false;
+ boolean changeStartSeq = false;
+ boolean changeEndRes = false;
+ boolean changeStartRes = false;
+ SequenceGroup stretchGroup = null;
+ boolean remove = false;
+
+ Point lastMousePress;
+ boolean mouseWheelPressed = false;
+ StringBuffer keyboardNo1;
+ StringBuffer keyboardNo2;
+
+ java.net.URL linkImageURL;
+
+ StringBuffer tooltipText = new StringBuffer("");
+ String tmpString;
+
+ EditCommand editCommand;
+
+ /**
+ * Creates a new SeqPanel object.
+ *
+ * @param avp DOCUMENT ME!
+ * @param p DOCUMENT ME!
+ */
+ public SeqPanel(AlignViewport avp, AlignmentPanel p)
+ {
+ linkImageURL = getClass().getResource("/images/link.gif");
+ ToolTipManager.sharedInstance().registerComponent(this);
+ ToolTipManager.sharedInstance().setInitialDelay(0);
+ ToolTipManager.sharedInstance().setDismissDelay(10000);
+ this.av = avp;
+ setBackground(Color.white);
+
+ seqCanvas = new SeqCanvas(avp);
+ setLayout(new BorderLayout());
+ add(seqCanvas, BorderLayout.CENTER);
+
+ ap = p;
+
+ if (!av.isDataset())
+ {
+ addMouseMotionListener(this);
+ addMouseListener(this);
+ addMouseWheelListener(this);
}
+ }
- int startWrapBlock=-1;
- int wrappedBlock=-1;
- int findRes(MouseEvent evt)
- {
- int res = 0;
- int x = evt.getX();
+ int startWrapBlock = -1;
+ int wrappedBlock = -1;
+ int findRes(MouseEvent evt)
+ {
+ int res = 0;
+ int x = evt.getX();
if (av.wrapAlignment)
{
int hgap = av.charHeight;
if (av.scaleAboveWrapped)
+ {
hgap += av.charHeight;
+ }
int cHeight = av.getAlignment().getHeight() * av.charHeight
+ hgap + seqCanvas.getAnnotationHeight();
- int y = evt.getY();
- y -= hgap;
- x -= seqCanvas.LABEL_WEST;
-
+ int y = evt.getY();
+ y -= hgap;
+ x -= seqCanvas.LABEL_WEST;
- int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
+ int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
+ if (cwidth < 1)
+ {
+ return 0;
+ }
- wrappedBlock = y / cHeight;
- wrappedBlock += av.getStartRes() / cwidth;
+ wrappedBlock = y / cHeight;
+ wrappedBlock += av.getStartRes() / cwidth;
- res = wrappedBlock * cwidth + x / av.getCharWidth();
+ res = wrappedBlock * cwidth + x / av.getCharWidth();
}
else
{
- res = (x / av.getCharWidth()) + av.getStartRes();
+ res = (x / av.getCharWidth()) + av.getStartRes();
}
- return res;
-
- }
+ if (av.hasHiddenColumns)
+ {
+ res = av.getColumnSelection().adjustForHiddenColumns(res);
+ }
- int findSeq(MouseEvent evt)
- {
+ return res;
- int seq = 0;
- int y = evt.getY();
+ }
- if (av.wrapAlignment)
- {
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
- hgap += av.charHeight;
+ int findSeq(MouseEvent evt)
+ {
+ int seq = 0;
+ int y = evt.getY();
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap + seqCanvas.getAnnotationHeight();
+ if (av.wrapAlignment)
+ {
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ {
+ hgap += av.charHeight;
+ }
- y -= hgap;
+ int cHeight = av.getAlignment().getHeight() * av.charHeight
+ + hgap + seqCanvas.getAnnotationHeight();
- seq = ( (y % cHeight) / av.getCharHeight());
- }
- else
- {
- seq = (y / av.getCharHeight()) + av.getStartSeq();
- }
+ y -= hgap;
- return seq;
- }
+ seq = Math.min( (y % cHeight) / av.getCharHeight(),
+ av.alignment.getHeight() - 1);
+ }
+ else
+ {
+ seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(),
+ av.alignment.getHeight() - 1);
+ }
+ return seq;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void doMouseReleased(MouseEvent evt)
+ SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+ {
+ Vector tmp = new Vector();
+ SequenceFeature[] features = sequence.getSequenceFeatures();
+ if (features != null)
{
- if (seqEditOccurred > -1)
+ for (int i = 0; i < features.length; i++)
+ {
+ if (av.featuresDisplayed == null
+ || !av.featuresDisplayed.containsKey(features[i].getType()))
{
- editOccurred(seqEditOccurred);
+ continue;
}
- startseq = -1;
- lastres = -1;
- seqEditOccurred = -1;
- editingSeqs = false;
- groupEditing = false;
-
- ap.repaint();
+ if ( (features[i].getBegin() <= res) &&
+ (features[i].getEnd() >= res))
+ {
+ tmp.addElement(features[i]);
+ }
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void doMousePressed(MouseEvent evt)
+ features = new SequenceFeature[tmp.size()];
+ for (int i = 0; i < tmp.size(); i++)
{
- ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
- av.alignment, HistoryItem.EDIT));
-
- int seq = findSeq(evt);
- int res = findRes(evt);
+ features[i] = (SequenceFeature) tmp.elementAt(i);
+ }
- if(seq<0 || res<0)
- return;
+ return features;
+ }
- if ((seq < av.getAlignment().getHeight()) &&
- (res < av.getAlignment().getSequenceAt(seq).getLength()))
- {
- startseq = seq;
- lastres = res;
- }
- else
+ Vector getAllFeaturesAtRes(SequenceI seq, int res)
+ {
+ Vector allFeatures = new Vector();
+ int index = 0;
+ if (seq.getSequenceFeatures() != null && av.featuresDisplayed != null)
+ {
+ while (index < seq.getSequenceFeatures().length)
+ {
+ SequenceFeature sf = seq.getSequenceFeatures()[index];
+ if (sf.getBegin() <= res &&
+ sf.getEnd() >= res)
{
- startseq = -1;
- lastres = -1;
+ if (av.featuresDisplayed.containsKey(sf.getType()))
+ {
+ allFeatures.addElement(sf);
+ }
}
-
- startEdit = lastres;
- endEdit = lastres;
-
- return;
+ index++;
+ }
}
+ return allFeatures;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void doMouseMoved(MouseEvent evt)
+ void endEditing()
+ {
+ if (editCommand != null && editCommand.getSize() > 0)
{
- int res = findRes(evt);
- int seq = findSeq(evt);
+ ap.alignFrame.addHistoryItem(editCommand);
+ av.firePropertyChange("alignment", null,
+ av.getAlignment().getSequences());
+ }
- if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
- return;
+ startseq = -1;
+ lastres = -1;
+ editingSeqs = false;
+ groupEditing = false;
+ keyboardNo1 = null;
+ keyboardNo2 = null;
+ editCommand = null;
+ }
+
+ void setCursorRow()
+ {
+ seqCanvas.cursorY = getKeyboardNo(keyboardNo1) - 1;
+ scrollToVisible();
+ }
+
+ void setCursorColumn()
+ {
+ seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
+ scrollToVisible();
+ }
+
+ void setCursorRowAndColumn()
+ {
+ if (keyboardNo2 == null)
+ {
+ keyboardNo2 = new StringBuffer();
+ }
+ else
+ {
+ seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1;
+ seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1;
+ scrollToVisible();
+ }
+ }
+
+ void setCursorPosition()
+ {
+ SequenceI sequence =
+ (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+ seqCanvas.cursorX = sequence.findIndex(
+ getKeyboardNo(keyboardNo1) - 1
+ );
+ scrollToVisible();
+ }
+
+ void moveCursor(int dx, int dy)
+ {
+ seqCanvas.cursorX += dx;
+ seqCanvas.cursorY += dy;
+ if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+ {
+ int original = seqCanvas.cursorX - dx;
+ int maxWidth = av.alignment.getWidth();
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ while (!av.colSel.isVisible(seqCanvas.cursorX)
+ && seqCanvas.cursorX < maxWidth
+ && seqCanvas.cursorX > 0)
+ {
+ seqCanvas.cursorX += dx;
+ }
- if (res > sequence.getLength())
+ if (seqCanvas.cursorX >= maxWidth
+ || !av.colSel.isVisible(seqCanvas.cursorX))
{
- return;
+ seqCanvas.cursorX = original;
}
+ }
- StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
- sequence.getName());
+ scrollToVisible();
+ }
- Object obj = null;
- if (av.alignment.isNucleotide())
- {
- obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
- "");
- if(obj!=null)
- text.append(" Nucleotide: ");
- }
- else
- {
- obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
- if(obj!=null)
- text.append(" Residue: ");
- }
+ void scrollToVisible()
+ {
+ if (seqCanvas.cursorX < 0)
+ {
+ seqCanvas.cursorX = 0;
+ }
+ else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+ {
+ seqCanvas.cursorX = av.alignment.getWidth() - 1;
+ }
- if (obj != null)
- {
+ if (seqCanvas.cursorY < 0)
+ {
+ seqCanvas.cursorY = 0;
+ }
+ else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+ {
+ seqCanvas.cursorY = av.alignment.getHeight() - 1;
+ }
- if (obj != "")
+ endEditing();
+ if (av.wrapAlignment)
+ {
+ ap.scrollToWrappedVisible(seqCanvas.cursorX);
+ }
+ else
+ {
+ while (seqCanvas.cursorY < av.startSeq)
+ {
+ ap.scrollUp(true);
+ }
+ while (seqCanvas.cursorY + 1 > av.endSeq)
+ {
+ ap.scrollUp(false);
+ }
+ if (!av.wrapAlignment)
+ {
+ while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
+ {
+ if (!ap.scrollRight(false))
{
- text.append( obj + " (" +
- av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+ break;
}
}
-
- ap.alignFrame.statusBar.setText(text.toString());
-
- // use aa to see if the mouse pointer is on a
- if (av.showSequenceFeatures)
+ while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
{
- Vector features = sequence.getSequenceFeatures();
- Enumeration e = features.elements();
- StringBuffer sbuffer = new StringBuffer();
-
- while (e.hasMoreElements())
- {
- SequenceFeature sf = (SequenceFeature) e.nextElement();
-
- if ((sf.getStart() <= sequence.findPosition(res)) &&
- (sf.getEnd() >= sequence.findPosition(res)))
- {
- if (sbuffer.length() > 0)
- {
- sbuffer.append("; ");
- }
-
- sbuffer.append(sf.getType() + " " + sf.getDescription());
-
- if (sf.getStatus().length() > 0)
- {
- sbuffer.append(" (" + sf.getStatus() + ")");
- }
- }
- }
-
- this.setToolTipText(sbuffer.toString());
+ if (!ap.scrollRight(true))
+ {
+ break;
+ }
}
+ }
}
+ setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+ seqCanvas.cursorX, seqCanvas.cursorY);
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void doMouseDragged(MouseEvent evt)
- {
- // If we're dragging we're editing
- int res = findRes(evt);
+ seqCanvas.repaint();
+ }
- if (res < 0)
+ void setSelectionAreaAtCursor(boolean topLeft)
+ {
+ SequenceI sequence =
+ (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+ if (av.getSelectionGroup() != null)
+ {
+ SequenceGroup sg = av.selectionGroup;
+ //Find the top and bottom of this group
+ int min = av.alignment.getHeight(), max = 0;
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ int index = av.alignment.findIndex(sg.getSequenceAt(i));
+ if (index > max)
{
- res = 0;
+ max = index;
}
-
- if ((lastres == -1) || (lastres == res))
+ if (index < min)
{
- return;
+ min = index;
}
+ }
- boolean dragRight = true;
+ max++;
- if ((res < av.getAlignment().getWidth()) && (res < lastres))
+ if (topLeft)
+ {
+ sg.setStartRes(seqCanvas.cursorX);
+ if (sg.getEndRes() < seqCanvas.cursorX)
{
- dragRight = false;
+ sg.setEndRes(seqCanvas.cursorX);
}
- if (res != lastres)
+ min = seqCanvas.cursorY;
+ }
+ else
+ {
+ sg.setEndRes(seqCanvas.cursorX);
+ if (sg.getStartRes() > seqCanvas.cursorX)
{
- // Group editing
- if (groupEditing)
- {
- SequenceGroup sg = av.getSelectionGroup();
-
- if (sg == null)
- {
- lastres = -1;
-
- return;
- }
-
- // drag to right
- if (dragRight)
- {
- sg.setEndRes(sg.getEndRes() + (res - lastres));
- }
+ sg.setStartRes(seqCanvas.cursorX);
+ }
- // drag to left
- else
- {
- /// Are we able to delete?
- // ie are all columns blank?
- boolean deleteAllowed = false;
-
- for (int s = 0; s < sg.getSize(); s++)
- {
- SequenceI seq = sg.getSequenceAt(s);
-
- for (int j = res; j < lastres; j++)
- {
- if (seq.getSequence().length() <= j)
- {
- continue;
- }
-
- if (!jalview.util.Comparison.isGap(
- seq.getSequence().charAt(j)))
- {
- // Not a gap, block edit not valid
- res = j + 1;
- deleteAllowed = false;
-
- continue;
- }
-
- deleteAllowed = true;
- }
- }
-
- if (!deleteAllowed)
- {
- lastres = -1;
-
- return;
- }
-
- sg.setEndRes(sg.getEndRes() - (lastres - res));
- }
+ max = seqCanvas.cursorY + 1;
+ }
- for (int i = 0; i < sg.getSize(); i++)
- {
- SequenceI s = sg.getSequenceAt(i);
- int k = av.alignment.findIndex(s);
-
- // drag to right
- if (dragRight)
- {
- for (int j = lastres; j < res; j++)
- {
- insertChar(j, k);
- }
- }
-
- // drag to left
- else
- {
- for (int j = res; j < lastres; j++)
- {
- if (s.getLength() > j)
- {
- deleteChar(res, k);
- }
- }
- }
- }
- }
- else /////Editing a single sequence///////////
- {
- if ((res < av.getAlignment().getWidth()) && (res > lastres))
- {
- // dragging to the right
- for (int j = lastres; j < res; j++)
- {
- insertChar(j, startseq);
- }
- }
- else if ((res < av.getAlignment().getWidth()) &&
- (res < lastres))
- {
- // dragging to the left
- for (int j = lastres; j > res; j--)
- {
- if (jalview.util.Comparison.isGap(
- av.alignment.getSequenceAt(startseq)
- .getSequence().charAt(res)))
- {
- deleteChar(res, startseq);
- }
- else
- {
- break;
- }
- }
- }
- }
+ if (min > max)
+ {
+ // Only the user can do this
+ av.setSelectionGroup(null);
+ }
+ else
+ {
+ // Now add any sequences between min and max
+ sg.getSequences(null).clear();
+ for (int i = min; i < max; i++)
+ {
+ sg.addSequence(av.alignment.getSequenceAt(i), false);
}
+ }
+ }
- endEdit = res;
- lastres = res;
- seqCanvas.repaint();
+ if (av.getSelectionGroup() == null)
+ {
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(seqCanvas.cursorX);
+ sg.setEndRes(seqCanvas.cursorX);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
}
- /**
- * DOCUMENT ME!
- *
- * @param seqstart DOCUMENT ME!
- * @param seqend DOCUMENT ME!
- * @param start DOCUMENT ME!
- */
- public void drawChars(int seqstart, int seqend, int start)
+ ap.repaint();
+ }
+
+ void insertGapAtCursor(boolean group)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(true, seqCanvas.cursorX + getKeyboardNo(keyboardNo1));
+ endEditing();
+ }
+
+ void deleteGapAtCursor(boolean group)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX + getKeyboardNo(keyboardNo1);
+ editSequence(false, seqCanvas.cursorX);
+ endEditing();
+ }
+
+ void numberPressed(char value)
+ {
+ if (keyboardNo1 == null)
{
- seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
- seqend, av.getStartRes(), av.getStartSeq(), 0);
- seqCanvas.repaint();
+ keyboardNo1 = new StringBuffer();
}
- /**
- * DOCUMENT ME!
- *
- * @param j DOCUMENT ME!
- * @param seq DOCUMENT ME!
- */
- public void insertChar(int j, int seq)
+ if (keyboardNo2 != null)
{
- av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());
- seqEditOccurred = seq;
+ keyboardNo2.append(value);
}
+ else
+ {
+ keyboardNo1.append(value);
+ }
+ }
- /**
- * DOCUMENT ME!
- *
- * @param j DOCUMENT ME!
- * @param seq DOCUMENT ME!
- */
- public void deleteChar(int j, int seq)
+ int getKeyboardNo(StringBuffer kb)
+ {
+ if (kb == null)
+ {
+ return 1;
+ }
+ else
+ {
+ return Integer.parseInt(kb.toString());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent evt)
+ {
+ mouseDragging = false;
+ mouseWheelPressed = false;
+
+ if (!editingSeqs)
{
- av.alignment.getSequenceAt(seq).deleteCharAt(j);
- seqEditOccurred = seq;
+ doMouseReleasedDefineMode(evt);
+ return;
+ }
+
+ endEditing();
+
+ ap.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mousePressed(MouseEvent evt)
+ {
+ lastMousePress = evt.getPoint();
- av.alignment.getWidth();
- seqCanvas.repaint();
+ if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+ {
+ mouseWheelPressed = true;
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- void editOccurred(int i)
+ if (evt.isShiftDown() || evt.isAltDown() ||
+ evt.isControlDown())
{
- if (endEdit == startEdit)
+ if (evt.isAltDown() || evt.isControlDown())
{
- ap.alignFrame.historyList.pop();
- ap.alignFrame.updateEditMenuBar();
+ groupEditing = true;
}
+ editingSeqs = true;
+ }
+ else
+ {
+ doMousePressedDefineMode(evt);
+ return;
+ }
+
+ int seq = findSeq(evt);
+ int res = findRes(evt);
+
+ if (seq < 0 || res < 0)
+ {
+ return;
+ }
- av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
+ if ( (seq < av.getAlignment().getHeight()) &&
+ (res < av.getAlignment().getSequenceAt(seq).getLength()))
+ {
+ startseq = seq;
+ lastres = res;
+ }
+ else
+ {
+ startseq = -1;
+ lastres = -1;
+ }
+ return;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent evt)
+ {
+ if (editingSeqs)
+ {
+ // This is because MacOSX creates a mouseMoved
+ // If control is down, other platforms will not.
+ mouseDragged(evt);
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void doMousePressedDefineMode(MouseEvent evt)
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+
+ if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
{
- int res = findRes(evt);
- int seq = findSeq(evt);
- oldSeq = seq;
+ return;
+ }
- startWrapBlock=wrappedBlock;
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- if(av.wrapAlignment && seq>av.alignment.getHeight())
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Cannot edit annotations in wrapped view.",
- "Wrapped view - no edit",
- JOptionPane.WARNING_MESSAGE);
- return;
- }
+ if (res > sequence.getLength())
+ {
+ return;
+ }
- if(seq<0 || res<0)
- return;
+ if (seqCanvas.pdbCanvas != null && sequence == seqCanvas.pdbCanvas.sequence)
+ {
+ seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+ }
+ setStatusMessage(sequence, res, seq);
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+ tooltipText.setLength(6); // Cuts the buffer back to
- if ((sequence == null) || (res > sequence.getLength()))
+ SequenceGroup[] groups = av.alignment.findAllGroups(sequence);
+ if (groups != null)
+ {
+ for (int g = 0; g < groups.length; g++)
+ {
+ if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
{
- return;
+ if (tooltipText.length() > 6)
+ {
+ tooltipText.append("
");
+ }
+
+ if (!groups[g].getName().startsWith("JTreeGroup") &&
+ !groups[g].getName().startsWith("JGroup"))
+ {
+ tooltipText.append(groups[g].getName());
+ }
+
+ if (groups[g].getDescription() != null)
+ {
+ tooltipText.append(": " + groups[g].getDescription());
+ }
}
+ }
+ }
- stretchGroup = av.getSelectionGroup();
+ // use aa to see if the mouse pointer is on a
+ if (av.showSequenceFeatures)
+ {
+ SequenceFeature[] features = findFeaturesAtRes(
+ sequence.getDatasetSequence(), sequence.findPosition(res));
- if (stretchGroup == null)
+ if (features != null)
+ {
+ for (int i = 0; i < features.length; i++)
{
- stretchGroup = av.alignment.findGroup(sequence);
-
- if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
- (res < stretchGroup.getEndRes()))
+ if (features[i].getType().equals("disulfide bond"))
+ {
+ if (features[i].getBegin() == sequence.findPosition(res)
+ || features[i].getEnd() == sequence.findPosition(res))
{
- av.setSelectionGroup(stretchGroup);
+ if (tooltipText.length() > 6)
+ {
+ tooltipText.append("
");
+ }
+ tooltipText.append("disulfide bond " + features[i].getBegin() +
+ ":" +
+ features[i].getEnd());
+ if (features[i].links != null)
+ {
+ tooltipText.append(" ![](\"")
");
+ }
}
- else
+ }
+ else
+ {
+ if (tooltipText.length() > 6)
{
- stretchGroup = null;
+ tooltipText.append("
");
}
- }
- else if (!stretchGroup.sequences.contains(sequence) ||
- (stretchGroup.getStartRes() > res) ||
- (stretchGroup.getEndRes() < res))
- {
- stretchGroup = null;
- SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+ tooltipText.append(features[i].getType() + " " +
+ features[i].begin);
+ if (features[i].begin != features[i].end)
+ {
+ tooltipText.append(" " + features[i].end);
+ }
- if (allGroups != null)
+ if (features[i].getDescription() != null
+ && !features[i].description.equals(features[i].getType()))
{
- for (int i = 0; i < allGroups.length; i++)
+ tmpString = features[i].getDescription();
+ int startTag = tmpString.toUpperCase().indexOf("");
+ if (startTag > -1)
+ {
+ tmpString = tmpString.substring(startTag + 6);
+ }
+ int endTag = tmpString.toUpperCase().indexOf("");
+ if (endTag > -1)
+ {
+ tmpString = tmpString.substring(0, endTag);
+ }
+ endTag = tmpString.toUpperCase().indexOf("");
+ if (endTag > -1)
+ {
+ tmpString = tmpString.substring(0, endTag);
+ }
+
+ if (startTag > -1)
+ {
+ tooltipText.append("; " + tmpString);
+ }
+ else
+ {
+ if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1)
{
- if ((allGroups[i].getStartRes() <= res) &&
- (allGroups[i].getEndRes() >= res))
- {
- stretchGroup = allGroups[i];
- av.setSelectionGroup(stretchGroup);
-
- break;
- }
- }
- }
- }
+ //The description does not specify html is to
+ //be used, so we must remove < > symbols
+ tmpString = tmpString.replaceAll("<", "<");
+ tmpString = tmpString.replaceAll(">", ">");
- if (stretchGroup == null)
- {
- // define a new group here
- SequenceGroup sg = new SequenceGroup();
- sg.setStartRes(res);
- sg.setEndRes(res);
- sg.addSequence(sequence, false);
- av.setSelectionGroup(sg);
- stretchGroup = sg;
+ tooltipText.append("; ");
+ tooltipText.append(tmpString);
- if (av.getConservationSelected())
+ }
+ else
+ {
+ tooltipText.append("; " + tmpString);
+ }
+ }
+ }
+ if (features[i].getValue("status") != null)
{
- SliderPanel.setConservationSlider(ap,
- av.getGlobalColourScheme(), "Background");
+ String status = features[i].getValue("status").toString();
+ if (status.length() > 0)
+ {
+ tooltipText.append("; (" + features[i].getValue("status") + ")");
+ }
}
- if (av.getAbovePIDThreshold())
+ if (features[i].links != null)
{
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
- "Background");
+ tooltipText.append(" ");
}
- }
- else if (javax.swing.SwingUtilities.isRightMouseButton(evt))
- {
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null);
- pop.show(this, evt.getX(), evt.getY());
- // edit the properties of existing group
- }
-
- if ((stretchGroup != null) && (stretchGroup.getEndRes() == res))
- {
- // Edit end res position of selected group
- changeEndRes = true;
- }
- else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res))
- {
- // Edit end res position of selected group
- changeStartRes = true;
+ }
}
-
- stretchGroup.getWidth();
-
- seqCanvas.repaint();
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void doMouseReleasedDefineMode(MouseEvent evt)
+ if (tooltipText.length() == 6) //
{
- if (mouseDragging)
- {
- stretchGroup.recalcConservation();
- mouseDragging = false;
- }
+ setToolTipText(null);
+ }
+ else
+ {
+ tooltipText.append("");
+ setToolTipText(tooltipText.toString());
+ }
+ // else
+ // setToolTipText(null);
+ }
- if (stretchGroup == null)
- {
- return;
+ void setStatusMessage(SequenceI sequence, int res, int seq)
+ {
+ StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+ sequence.getName());
+
+ Object obj = null;
+ if (av.alignment.isNucleotide())
+ {
+ obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+ "");
+ if (obj != null)
+ {
+ text.append(" Nucleotide: ");
+ }
+ }
+ else
+ {
+ obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+ if (obj != null)
+ {
+ text.append(" Residue: ");
+ }
+ }
+
+ if (obj != null)
+ {
+
+ if (obj != "")
+ {
+ text.append(obj + " (" + sequence.findPosition(res) +
+ ")");
+ }
+ }
+ ap.alignFrame.statusBar.setText(text.toString());
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (mouseWheelPressed)
+ {
+ int oldWidth = av.charWidth;
+
+ //Which is bigger, left-right or up-down?
+ if (Math.abs(evt.getY() - lastMousePress.getY())
+ > Math.abs(evt.getX() - lastMousePress.getX()))
+ {
+ int fontSize = av.font.getSize();
+
+ if (evt.getY() < lastMousePress.getY())
+ {
+ fontSize--;
+ }
+ else if (evt.getY() > lastMousePress.getY())
+ {
+ fontSize++;
}
- if(stretchGroup.cs!=null)
+ if (fontSize < 1)
{
- if (stretchGroup.cs instanceof ClustalxColourScheme)
- {
- ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
- sequences,
- stretchGroup.getWidth());
- }
+ fontSize = 1;
+ }
- if (stretchGroup.cs.conservationApplied())
- {
- SliderPanel.setConservationSlider(ap, stretchGroup.cs,
- stretchGroup.getName());
- }
- else
- {
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
- stretchGroup.getName());
- }
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+ av.charWidth = oldWidth;
+ ap.fontChanged();
+ }
+ else
+ {
+ if (evt.getX() < lastMousePress.getX() && av.charWidth > 1)
+ {
+ av.charWidth--;
}
- changeEndRes = false;
- changeStartRes = false;
- stretchGroup = null;
- PaintRefresher.Refresh(av.alignment);
+ else if (evt.getX() > lastMousePress.getX())
+ {
+ av.charWidth++;
+ }
+
+ ap.repaint();
+ }
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+ av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+
+ lastMousePress = evt.getPoint();
+
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void doMouseDraggedDefineMode(MouseEvent evt)
+ if (!editingSeqs)
{
- int res = findRes(evt);
- int y = findSeq(evt);
+ doMouseDraggedDefineMode(evt);
+ return;
+ }
- if(wrappedBlock!=startWrapBlock)
- return;
+ int res = findRes(evt);
+
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ if ( (lastres == -1) || (lastres == res))
+ {
+ return;
+ }
+
+ if ( (res < av.getAlignment().getWidth()) && (res < lastres))
+ {
+ // dragLeft, delete gap
+ editSequence(false, res);
+ }
+ else
+ {
+ editSequence(true, res);
+ }
+
+ mouseDragging = true;
+ if (scrollThread != null)
+ {
+ scrollThread.setEvent(evt);
+ }
+
+ }
+
+ synchronized void editSequence(boolean insertGap, int startres)
+ {
+ int fixedLeft = -1;
+ int fixedRight = -1;
+ boolean fixedColumns = false;
+ SequenceGroup sg = av.getSelectionGroup();
- if (stretchGroup == null)
+ SequenceI seq = av.alignment.getSequenceAt(startseq);
+
+ //No group, but the sequence may represent a group
+ if (!groupEditing && av.hasHiddenRows)
+ {
+ if (av.hiddenRepSequences != null
+ && av.hiddenRepSequences.containsKey(seq))
{
- return;
- }
+ sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ groupEditing = true;
+ }
+ }
+
+ StringBuffer message = new StringBuffer();
+ if (groupEditing)
+ {
+ message.append("Edit group:");
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand("Edit Group");
+ }
+ }
+ else
+ {
+ message.append("Edit sequence: " + seq.getName());
+ String label = seq.getName();
+ if (label.length() > 10)
+ {
+ label = label.substring(0, 10);
+ }
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand("Edit " + label);
+ }
+ }
+
+ if (insertGap)
+ {
+ message.append(" insert ");
+ }
+ else
+ {
+ message.append(" delete ");
+ }
+
+ message.append(Math.abs(startres - lastres) + " gaps.");
+ ap.alignFrame.statusBar.setText(message.toString());
- if (res > av.alignment.getWidth())
+ //Are we editing within a selection group?
+ if (groupEditing
+ || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq)))
+ {
+ fixedColumns = true;
+
+ //sg might be null as the user may only see 1 sequence,
+ //but the sequence represents a group
+ if (sg == null)
+ {
+ if (av.hiddenRepSequences == null
+ || !av.hiddenRepSequences.containsKey(seq))
{
- res = av.alignment.getWidth() - 1;
+ endEditing();
+ return;
}
+ sg = (SequenceGroup) av.hiddenRepSequences.get(seq);
+ }
+
+ fixedLeft = sg.getStartRes();
+ fixedRight = sg.getEndRes();
+
+ if ( (startres < fixedLeft && lastres >= fixedLeft)
+ || (startres >= fixedLeft && lastres < fixedLeft)
+ || (startres > fixedRight && lastres <= fixedRight)
+ || (startres <= fixedRight && lastres > fixedRight))
+ {
+ endEditing();
+ return;
+ }
+
+ if (fixedLeft > startres)
+ {
+ fixedRight = fixedLeft - 1;
+ fixedLeft = 0;
+ }
+ else if (fixedRight < startres)
+ {
+ fixedLeft = fixedRight;
+ fixedRight = -1;
+ }
+ }
- if (stretchGroup.getEndRes() == res)
+ if (av.hasHiddenColumns)
+ {
+ fixedColumns = true;
+ int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres);
+ int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres);
+
+ if ( (insertGap && startres > y1 && lastres < y1)
+ || (!insertGap && startres < y2 && lastres > y2))
+ {
+ endEditing();
+ return;
+ }
+
+ //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~");
+ //Selection spans a hidden region
+ if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1))
+ {
+ if (startres >= y2)
{
- // Edit end res position of selected group
- changeEndRes = true;
+ fixedLeft = y2;
}
- else if (stretchGroup.getStartRes() == res)
+ else
{
- // Edit start res position of selected group
- changeStartRes = true;
+ fixedRight = y2 - 1;
}
+ }
+ }
- if (res < av.getStartRes())
+ 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);
+ }
+
+ // drag to right
+ if (insertGap)
+ {
+ //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
+ )
{
- res = av.getStartRes();
+ sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+ fixedRight = sg.getEndRes();
}
- else if (res > av.getEndRes() && !av.getWrapAlignment())
+
+ // Is it valid with fixed columns??
+ // Find the next gap before the end
+ // of the visible region boundary
+ boolean blank = false;
+ for (fixedRight = fixedRight;
+ fixedRight > lastres;
+ fixedRight--)
{
- res = av.getEndRes();
+ blank = true;
+
+ for (g = 0; g < groupSize; g++)
+ {
+ for (int j = 0; j < startres - lastres; j++)
+ {
+ if (!jalview.util.Comparison.isGap(
+ groupSeqs[g].getCharAt(fixedRight - j)))
+ {
+ blank = false;
+ break;
+ }
+ }
+ }
+ if (blank)
+ {
+ break;
+ }
}
- if (changeEndRes)
+ if (!blank)
{
- if (res > (stretchGroup.getStartRes() - 1))
+ if (sg.getSize() == av.alignment.getHeight())
+ {
+ if ( (av.hasHiddenColumns
+ &&
+ startres < av.getColumnSelection().getHiddenBoundaryRight(startres)))
{
- stretchGroup.setEndRes(res);
+ endEditing();
+ return;
}
+
+ int alWidth = av.alignment.getWidth();
+ if (av.hasHiddenRows)
+ {
+ int hwidth = av.alignment.getHiddenSequences().getWidth();
+ if (hwidth > alWidth)
+ {
+ alWidth = hwidth;
+ }
+ }
+ //We can still insert gaps if the selectionGroup
+ //contains all the sequences
+ sg.setEndRes(sg.getEndRes() + startres - lastres);
+ fixedRight = alWidth + startres - lastres;
+ }
+ else
+ {
+ endEditing();
+ return;
+ }
}
- else if (changeStartRes)
+ }
+
+ // drag to left
+ else if (!insertGap)
+ {
+ /// Are we able to delete?
+ // ie are all columns blank?
+
+ for (g = 0; g < groupSize; g++)
{
- if (res < (stretchGroup.getEndRes() + 1))
+ for (int j = startres; j < lastres; j++)
+ {
+ if (groupSeqs[g].getLength() <= j)
{
- stretchGroup.setStartRes(res);
+ continue;
}
- }
- int dragDirection = 0;
+ if (!jalview.util.Comparison.isGap(
+ groupSeqs[g].getCharAt(j)))
+ {
+ // Not a gap, block edit not valid
+ endEditing();
+ return;
+ }
+ }
+ }
+ }
- if (y > oldSeq)
+ if (insertGap)
+ {
+ // dragging to the right
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j < startres; j++)
+ {
+ insertChar(j, groupSeqs, fixedRight);
+ }
+ }
+ else
{
- dragDirection = 1;
+ editCommand.appendEdit(EditCommand.INSERT_GAP,
+ groupSeqs,
+ startres, startres - lastres,
+ av.alignment,
+ true);
}
- else if (y < oldSeq)
+ }
+ else
+ {
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
{
- dragDirection = -1;
+ for (int j = lastres; j > startres; j--)
+ {
+ deleteChar(startres, groupSeqs, fixedRight);
+ }
}
-
- while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight()))
+ else
{
- // This routine ensures we don't skip any sequences, as the
- // selection is quite slow.
- Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
-
- oldSeq += dragDirection;
-
- Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+ editCommand.appendEdit(EditCommand.DELETE_GAP,
+ groupSeqs,
+ startres, lastres - startres,
+ av.alignment,
+ true);
+ }
- if (stretchGroup.sequences.contains(nextSeq))
+ }
+ }
+ else /////Editing a single sequence///////////
+ {
+ if (insertGap)
+ {
+ // dragging to the right
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j < startres; j++)
+ {
+ insertChar(j, new SequenceI[]
+ {seq}, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.INSERT_GAP,
+ new SequenceI[]
+ {seq},
+ lastres, startres - lastres,
+ av.alignment,
+ true);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j > startres; j--)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(startres)))
{
- stretchGroup.deleteSequence(seq, false);
+ endEditing();
+ break;
}
- else
+ 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)))
{
- if (seq != null)
- {
- stretchGroup.addSequence(seq, false);
- }
-
- stretchGroup.addSequence(nextSeq, false);
+ break;
}
+ max++;
+ }
+
+ if (max > 0)
+ {
+ editCommand.appendEdit(EditCommand.DELETE_GAP,
+ new SequenceI[]
+ {seq},
+ startres, max,
+ av.alignment,
+ true);
+ }
}
+ }
+ }
+
+ lastres = startres;
+ seqCanvas.repaint();
+ }
- oldSeq = y;
- mouseDragging = true;
+ void insertChar(int j, SequenceI[] seq, int fixedColumn)
+ {
+ int blankColumn = fixedColumn;
+ for (int s = 0; s < seq.length; s++)
+ {
+ //Find the next gap before the end of the visible region boundary
+ //If lastCol > j, theres a boundary after the gap insertion
- if (scrollThread != null)
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+ {
+ if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
{
- scrollThread.setEvent(evt);
+ //Theres a space, so break and insert the gap
+ break;
}
+ }
- seqCanvas.repaint();
+ if (blankColumn <= j)
+ {
+ blankColumn = fixedColumn;
+ endEditing();
+ return;
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void doMouseEnteredDefineMode(MouseEvent e)
+ editCommand.appendEdit(EditCommand.DELETE_GAP,
+ seq,
+ blankColumn, 1, av.alignment, true);
+
+ editCommand.appendEdit(EditCommand.INSERT_GAP,
+ seq,
+ j, 1, av.alignment,
+ true);
+
+ }
+
+ void deleteChar(int j, SequenceI[] seq, int fixedColumn)
+ {
+
+ editCommand.appendEdit(EditCommand.DELETE_GAP,
+ seq,
+ j, 1, av.alignment, true);
+
+ editCommand.appendEdit(EditCommand.INSERT_GAP,
+ seq,
+ fixedColumn, 1, av.alignment, true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent e)
+ {
+ if (oldSeq < 0)
{
- if (scrollThread != null)
- {
- scrollThread.running = false;
- }
+ oldSeq = 0;
+ }
+
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging)
+ {
+ scrollThread = new ScrollThread();
+ }
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt));
+ if (evt.getClickCount() > 1)
+ {
+ if (av.getSelectionGroup().getSize() == 1
+ && av.getSelectionGroup().getEndRes()
+ - av.getSelectionGroup().getStartRes() < 2)
+ {
+ av.setSelectionGroup(null);
+ }
+
+ SequenceFeature[] features = findFeaturesAtRes(
+ sequence.getDatasetSequence(),
+ sequence.findPosition(findRes(evt))
+ );
+
+ if (features != null && features.length > 0)
+ {
+ SearchResults highlight = new SearchResults();
+ highlight.addResult(sequence,
+ features[0].getBegin(),
+ features[0].getEnd());
+ seqCanvas.highlightSearchResults(highlight);
+ }
+ if (features != null && features.length > 0)
+ {
+ seqCanvas.getFeatureRenderer().amendFeatures(
+ new SequenceI[]
+ {sequence}, features, false, ap);
+
+ seqCanvas.highlightSearchResults(null);
+ }
+ }
+ }
+
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ e.consume();
+ /* if (mouseWheelPressed)
+ {
+ Font font = av.getFont();
+ int fontSize = font.getSize();
+ if (e.getWheelRotation() > 0 && fontSize < 51)
+ fontSize++;
+ else if (fontSize > 1)
+ fontSize--;
+
+
+
+ av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
+
+ ap.fontChanged();
+ }
+ else*/
+ {
+ if (e.getWheelRotation() > 0)
+ {
+ ap.scrollUp(false);
+ }
+ else
+ {
+ ap.scrollUp(true);
+ }
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void doMousePressedDefineMode(MouseEvent evt)
+ {
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+ oldSeq = seq;
+
+ startWrapBlock = wrappedBlock;
+
+ if (av.wrapAlignment && seq > av.alignment.getHeight())
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Cannot edit annotations in wrapped view.",
+ "Wrapped view - no edit",
+ JOptionPane.WARNING_MESSAGE);
+ return;
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void doMouseExitedDefineMode(MouseEvent e)
+ if (seq < 0 || res < 0)
+ {
+ return;
+ }
+
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+
+ if ( (sequence == null) || (res > sequence.getLength()))
+ {
+ return;
+ }
+
+ stretchGroup = av.getSelectionGroup();
+
+ if (stretchGroup == null)
+ {
+ stretchGroup = av.alignment.findGroup(sequence);
+
+ if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) &&
+ (res < stretchGroup.getEndRes()))
+ {
+ av.setSelectionGroup(stretchGroup);
+ }
+ else
+ {
+ stretchGroup = null;
+ }
+ }
+ else if (!stretchGroup.getSequences(null).contains(sequence) ||
+ (stretchGroup.getStartRes() > res) ||
+ (stretchGroup.getEndRes() < res))
{
- if (av.getWrapAlignment())
+ stretchGroup = null;
+
+ SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+
+ if (allGroups != null)
+ {
+ for (int i = 0; i < allGroups.length; i++)
{
- return;
+ if ( (allGroups[i].getStartRes() <= res) &&
+ (allGroups[i].getEndRes() >= res))
+ {
+ stretchGroup = allGroups[i];
+ break;
+ }
}
+ }
+
+ av.setSelectionGroup(stretchGroup);
- if (mouseDragging)
+ }
+
+ if (javax.swing.SwingUtilities.isRightMouseButton(evt))
+ {
+ Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(),
+ sequence.findPosition(res));
+ Vector links = new Vector();
+ for (int i = 0; i < allFeatures.size(); i++)
+ {
+ SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
+ if (sf.links != null)
{
- scrollThread = new ScrollThread();
+ for (int j = 0; j < sf.links.size(); j++)
+ {
+ links.addElement(sf.links.elementAt(j));
+ }
}
+ }
+
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links);
+ pop.show(this, evt.getX(), evt.getY());
+ return;
+ }
+
+ if (av.cursorMode)
+ {
+ seqCanvas.cursorX = findRes(evt);
+ seqCanvas.cursorY = findSeq(evt);
+ seqCanvas.repaint();
+ return;
+ }
+
+ if (stretchGroup == null)
+ {
+ //Only if left mouse button do we want to change group sizes
+
+ // define a new group here
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(res);
+ sg.setEndRes(res);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
+ stretchGroup = sg;
+
+ if (av.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(ap,
+ av.getGlobalColourScheme(),
+ "Background");
+ }
+
+ if (av.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+ "Background");
+ }
+ if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res))
+ {
+ // Edit end res position of selected group
+ changeEndRes = true;
+ }
+ else if ( (stretchGroup != null) &&
+ (stretchGroup.getStartRes() == res))
+ {
+ // Edit end res position of selected group
+ changeStartRes = true;
+ }
+ stretchGroup.getWidth();
+ }
+
+ seqCanvas.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void doMouseReleasedDefineMode(MouseEvent evt)
+ {
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ 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();
+ }
+
+ if (stretchGroup.cs.conservationApplied())
+ {
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ }
+ else
+ {
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ }
+ }
+ changeEndRes = false;
+ changeStartRes = false;
+ stretchGroup = null;
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void doMouseDraggedDefineMode(MouseEvent evt)
+ {
+ int res = findRes(evt);
+ int y = findSeq(evt);
+
+ if (wrappedBlock != startWrapBlock)
+ {
+ return;
+ }
+
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ if (res >= av.alignment.getWidth())
+ {
+ res = av.alignment.getWidth() - 1;
+ }
+
+ if (stretchGroup.getEndRes() == res)
+ {
+ // Edit end res position of selected group
+ changeEndRes = true;
+ }
+ else if (stretchGroup.getStartRes() == res)
+ {
+ // Edit start res position of selected group
+ changeStartRes = true;
+ }
+
+ if (res < av.getStartRes())
+ {
+ res = av.getStartRes();
+ }
+
+ if (changeEndRes)
+ {
+ if (res > (stretchGroup.getStartRes() - 1))
+ {
+ stretchGroup.setEndRes(res);
+ }
+ }
+ else if (changeStartRes)
+ {
+ if (res < (stretchGroup.getEndRes() + 1))
+ {
+ stretchGroup.setStartRes(res);
+ }
}
- // this class allows scrolling off the bottom of the visible alignment
- class ScrollThread extends Thread
+ int dragDirection = 0;
+
+ if (y > oldSeq)
{
- MouseEvent evt;
- boolean running = false;
+ dragDirection = 1;
+ }
+ else if (y < oldSeq)
+ {
+ dragDirection = -1;
+ }
+
+ while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight()))
+ {
+ // This routine ensures we don't skip any sequences, as the
+ // selection is quite slow.
+ Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+ oldSeq += dragDirection;
+
+ if (oldSeq < 0)
+ {
+ break;
+ }
- public ScrollThread()
+ Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+ if (stretchGroup.getSequences(null).contains(nextSeq))
+ {
+ stretchGroup.deleteSequence(seq, false);
+ }
+ else
+ {
+ if (seq != null)
{
- start();
+ stretchGroup.addSequence(seq, false);
}
- public void setEvent(MouseEvent e)
+ stretchGroup.addSequence(nextSeq, false);
+ }
+ }
+
+ if (oldSeq < 0)
+ {
+ oldSeq = -1;
+ }
+
+ mouseDragging = true;
+
+ if (scrollThread != null)
+ {
+ scrollThread.setEvent(evt);
+ }
+
+ seqCanvas.repaint();
+ }
+
+ void scrollCanvas(MouseEvent evt)
+ {
+ if (evt == null)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+ mouseDragging = false;
+ }
+ else
+ {
+ if (scrollThread == null)
+ {
+ scrollThread = new ScrollThread();
+ }
+
+ mouseDragging = true;
+ scrollThread.setEvent(evt);
+ }
+
+ }
+
+ // this class allows scrolling off the bottom of the visible alignment
+ class ScrollThread
+ extends Thread
+ {
+ MouseEvent evt;
+ boolean running = false;
+
+ public ScrollThread()
+ {
+ start();
+ }
+
+ public void setEvent(MouseEvent e)
+ {
+ evt = e;
+ }
+
+ public void stopScrolling()
+ {
+ running = false;
+ }
+
+ public void run()
+ {
+ running = true;
+
+ while (running)
+ {
+ if (evt != null)
{
- evt = e;
+ if (mouseDragging && (evt.getY() < 0) &&
+ (av.getStartSeq() > 0))
+ {
+ running = ap.scrollUp(true);
+ }
+
+ if (mouseDragging && (evt.getY() >= getHeight()) &&
+ (av.alignment.getHeight() > av.getEndSeq()))
+ {
+ running = ap.scrollUp(false);
+ }
+
+ if (mouseDragging && (evt.getX() < 0))
+ {
+ running = ap.scrollRight(false);
+ }
+ else if (mouseDragging && (evt.getX() >= getWidth()))
+ {
+ running = ap.scrollRight(true);
+ }
}
- public void stopScrolling()
+ try
{
- running = false;
+ Thread.sleep(20);
}
-
- public void run()
+ catch (Exception ex)
{
- running = true;
-
- while (running)
- {
- if (evt != null)
- {
- if (mouseDragging && (evt.getY() < 0) &&
- (av.getStartSeq() > 0))
- {
- running = ap.scrollUp(true);
- }
-
- if (mouseDragging && (evt.getY() >= getHeight()) &&
- (av.alignment.getHeight() > av.getEndSeq()))
- {
- running = ap.scrollUp(false);
- }
-
- if (mouseDragging && (evt.getX() < 0))
- {
- running = ap.scrollRight(true);
- }
- else if (mouseDragging && (evt.getX() >= getWidth()))
- {
- running = ap.scrollRight(false);
- }
- }
-
- try
- {
- Thread.sleep(75);
- }
- catch (Exception ex)
- {
- }
- }
}
+ }
}
+ }
}