-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import jalview.datamodel.*;\r
-import javax.swing.*;\r
-import java.util.*;\r
-import jalview.schemes.*;\r
-\r
-public class SeqPanel extends JPanel\r
-{\r
-\r
- public SeqCanvas seqCanvas;\r
- public AlignmentPanel ap;\r
-\r
- protected int startres;\r
- protected int lastres;\r
- protected int endres;\r
-\r
- protected int startseq;\r
- protected int padseq;\r
-\r
- protected AlignViewport av;\r
-\r
- // if character is inserted or deleted, we will need to recalculate the conservation\r
- int seqEditOccurred = -1;\r
-\r
- ScrollThread scrollThread = null;\r
- boolean mouseDragging = false;\r
-\r
-\r
- public SeqPanel(AlignViewport avp, AlignmentPanel p) {\r
- this.av = avp;\r
-\r
- seqCanvas = new SeqCanvas(avp);\r
- setLayout(new BorderLayout());\r
- add(seqCanvas, BorderLayout.CENTER);\r
-\r
- ap = p;\r
-\r
- addMouseMotionListener( new MouseMotionAdapter()\r
- {\r
- public void mouseMoved(MouseEvent evt)\r
- {\r
- if(av.getWrapAlignment())\r
- return;\r
- doMouseMoved(evt); }\r
-\r
- public void mouseDragged(MouseEvent evt)\r
- {\r
- if(av.getWrapAlignment())\r
- return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
- doMouseDragged(evt);\r
- else\r
- doMouseDraggedDefineMode(evt);\r
- }\r
- });\r
-\r
- addMouseListener( new MouseAdapter()\r
- {\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- if(av.getWrapAlignment())\r
- return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
- doMouseReleased(evt);\r
- else\r
- doMouseReleasedDefineMode(evt);\r
- }\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if(av.getWrapAlignment())\r
- return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
- doMousePressed(evt);\r
- else\r
- doMousePressedDefineMode(evt);\r
- }\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
- return;\r
- doMouseExitedDefineMode(evt);\r
-\r
- }\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
- return;\r
- doMouseEnteredDefineMode(evt);\r
- }\r
-\r
- });\r
- repaint();\r
- }\r
-\r
-\r
- public void doMouseReleased(MouseEvent evt) {\r
-\r
- int x = evt.getX();\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
-\r
- endres = res;\r
-\r
- startseq = -1;\r
- startres = -1;\r
- lastres = -1;\r
- if(seqEditOccurred>-1)\r
- updateConservation(seqEditOccurred);\r
-\r
- seqEditOccurred = -1;\r
-\r
- ap.repaint();\r
-\r
- }\r
-\r
- public void doMousePressed(MouseEvent evt) {\r
- ap.alignFrame.addHistoryItem("sequence edit");\r
- int seq;\r
- int res;\r
-\r
- int x = evt.getX();\r
- int y = evt.getY();\r
-\r
- res = x/av.getCharWidth() + av.getStartRes();\r
- seq = y/av.getCharHeight() + av.getStartSeq();\r
-\r
- if (seq < av.getAlignment().getHeight() &&\r
- res < av.getAlignment().getSequenceAt(seq).getLength())\r
- {\r
- //char resstr = align.getSequenceAt(seq).getSequence().charAt(res);\r
- // Find the residue's position in the sequence (res is the position\r
- // in the alignment\r
-\r
- startseq = seq;\r
-\r
- if (startseq == (av.getAlignment().getHeight() - 1))\r
- padseq = 1;\r
- else\r
- padseq = 1;\r
-\r
- startres = res;\r
- lastres = res;\r
-\r
- }\r
- else\r
- {\r
- startseq = -1;\r
- startres = -1;\r
- lastres = -1;\r
- }\r
-\r
- return;\r
- }\r
-\r
- public void doMouseMoved(MouseEvent evt)\r
- {\r
- int res=0, seq=0;\r
- int x = evt.getX();\r
- int y = evt.getY();\r
- if(av.wrapAlignment)\r
- {\r
- y -= 2*av.charHeight;\r
- int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight;\r
-\r
-\r
- res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes();\r
-\r
- y %= chunkHeight;\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
-\r
- }\r
- else\r
- {\r
- res = x / av.getCharWidth() + av.getStartRes();\r
- seq = y / av.getCharHeight() + av.getStartSeq();\r
- }\r
-\r
-\r
- if(seq>=av.getAlignment().getHeight())\r
- return;\r
-\r
- SequenceI sequence = av.getAlignment().getSequenceAt(seq);\r
- if(res>sequence.getLength())\r
- return;\r
-\r
- Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;\r
- String aa = "";\r
- if(obj!=null)\r
- aa = obj.toString();\r
-\r
- StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());\r
- if(aa!="")\r
- text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")");\r
-\r
- ap.alignFrame.statusBar.setText(text.toString());\r
-\r
- // use aa to see if the mouse pointer is on a\r
- if( av.showSequenceFeatures)\r
- {\r
- Vector features = sequence.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- StringBuffer sbuffer = new StringBuffer();\r
-\r
-\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- if (sf.getStart() <= sequence.findPosition(res) &&\r
- sf.getEnd() >= sequence.findPosition(res))\r
- {\r
- if(sbuffer.length()>0)\r
- sbuffer.append("; ");\r
- sbuffer.append(sf.getType() + " " + sf.getDescription());\r
- if(sf.getStatus().length()>0)\r
- sbuffer.append(" ("+sf.getStatus()+")");\r
- }\r
-\r
- }\r
-\r
- ToolTipManager.sharedInstance().registerComponent(this);\r
- this.setToolTipText(sbuffer.toString());\r
- }\r
-\r
-\r
- }\r
-\r
- public void doMouseDragged(MouseEvent evt) {\r
- // If we're dragging we're editing\r
-\r
- if(lastres==-1)\r
- return;\r
-\r
- int x = evt.getX();\r
-\r
- int res = x/av.getCharWidth() + av.getStartRes();\r
- if (res < 0)\r
- res = 0;\r
-\r
- if (res != lastres)\r
- {\r
- // Group editing\r
- if (evt.isAltDown() || evt.isControlDown())\r
- {\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if(sg==null)\r
- av.getAlignment().findGroup(startseq);\r
- if (sg != null)\r
- {\r
- boolean deleteAllowed = false;\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
- {\r
- /// Are we able to delete?\r
- boolean allGaps = true;\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI s = sg.getSequenceAt(i);\r
- for (int j = lastres-1; j >= res && allGaps; j--)\r
- {\r
- if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j)))\r
- {\r
- res = j + 1;\r
- allGaps = false;\r
- }\r
- }\r
-\r
- if(!deleteAllowed && allGaps)\r
- deleteAllowed = true;\r
- }\r
- }\r
-\r
- // drag to right\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
- sg.setEndRes(sg.getEndRes() + 1);\r
-\r
- // drag to left\r
- else if (deleteAllowed && res < av.getAlignment().getWidth() &&\r
- res < lastres)\r
- sg.setEndRes(sg.getEndRes() - 1);\r
-\r
-\r
-\r
-\r
- for (int i = 0; i < sg.getSize(); i++)\r
- {\r
- SequenceI s = sg.getSequenceAt(i);\r
- int k = av.alignment.findIndex(s);\r
-\r
- // drag to right\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, k);\r
-\r
- // drag to left\r
- else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres)\r
- {\r
- for (int j = res; j < lastres; j++)\r
- {\r
- deleteChar(j, k);\r
- startres = res;\r
- }\r
- }\r
- }\r
- }\r
- }\r
- else /////Editing a single sequence///////////\r
- {\r
- if (res < av.getAlignment().getWidth() && res > lastres)\r
- {\r
- // dragging to the right\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, startseq);\r
- }\r
- else if (res < av.getAlignment().getWidth() && res < lastres)\r
- {\r
- // dragging to the left\r
- for (int j = res; j < lastres; j++)\r
- {\r
- deleteChar(j, startseq);\r
- startres = res;\r
- }\r
- }\r
-\r
- }\r
-\r
- }\r
-\r
- lastres = res;\r
- repaint();\r
- }\r
-\r
- public void drawChars(int seqstart, int seqend, int start) {\r
- seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0);\r
- repaint();\r
- }\r
-\r
- public void insertChar(int j, int seq)\r
- {\r
- av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter());\r
- seqEditOccurred=seq;\r
- }\r
-\r
- public void deleteChar(int j, int seq)\r
- {\r
-\r
- if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))\r
- av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
-\r
- av.alignment.getWidth();\r
- repaint();\r
- seqEditOccurred=seq;\r
- }\r
-\r
-\r
- void updateConservation(int i)\r
- {\r
- if(av.getGlobalColourScheme() instanceof jalview.schemes.ClustalxColourScheme)\r
- {\r
- av.setGlobalColourScheme(\r
- new jalview.schemes.ClustalxColourScheme(av.alignment.getSequences(),av.alignment.getWidth() ));\r
- }\r
- av.updateConservation();\r
- av.updateConsensus();\r
- }\r
-\r
-//////////////////////////////////////////\r
-/////Everything below this is for defining the boundary of the rubberband\r
-//////////////////////////////////////////\r
- int oldSeq = -1;\r
- public void doMousePressedDefineMode(MouseEvent evt)\r
- {\r
- int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
- oldSeq = seq;\r
-\r
- SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);\r
-\r
- if(sequence==null || res>sequence.getLength())\r
- return;\r
-\r
- stretchGroup = av.getSelectionGroup();\r
-\r
- if(stretchGroup == null)\r
- {\r
- stretchGroup = av.alignment.findGroup( sequence );\r
- if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())\r
- av.setSelectionGroup(stretchGroup);\r
- else\r
- stretchGroup = null;\r
- }\r
-\r
- else if(!stretchGroup.sequences.contains(sequence)\r
- || stretchGroup.getStartRes()>res\r
- || stretchGroup.getEndRes()<res)\r
- {\r
- stretchGroup = null;\r
-\r
- SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );\r
-\r
- if (allGroups != null)\r
- for (int i = 0; i < allGroups.length; i++)\r
- if (allGroups[i].getStartRes() <= res &&\r
- allGroups[i].getEndRes() >= res)\r
- {\r
- stretchGroup = allGroups[i];\r
- av.setSelectionGroup(stretchGroup);\r
- break;\r
- }\r
- }\r
-\r
- if(stretchGroup==null)\r
- {\r
- // define a new group here\r
- SequenceGroup sg = new SequenceGroup();\r
- sg.setStartRes(res);\r
- sg.setEndRes(res);\r
- sg.addSequence( sequence );\r
- av.setSelectionGroup( sg );\r
- stretchGroup = sg;\r
-\r
- if(av.getConservationSelected())\r
- SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");\r
- if(av.getAbovePIDThreshold())\r
- SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");\r
-\r
- }\r
- else if( javax.swing.SwingUtilities.isRightMouseButton(evt))\r
- {\r
- jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);\r
- pop.show(this, evt.getX(), evt.getY());\r
-\r
- // edit the properties of existing group\r
- }\r
-\r
- if(stretchGroup!=null && stretchGroup.getEndRes()==res)\r
- // Edit end res position of selected group\r
- changeEndRes = true;\r
-\r
- else if(stretchGroup!=null && stretchGroup.getStartRes()==res)\r
- // Edit end res position of selected group\r
- changeStartRes = true;\r
-\r
-\r
- repaint();\r
-\r
- }\r
-\r
- boolean changeEndSeq = false;\r
- boolean changeStartSeq = false;\r
- boolean changeEndRes = false;\r
- boolean changeStartRes = false;\r
- SequenceGroup stretchGroup = null;\r
-\r
- public void doMouseReleasedDefineMode(MouseEvent evt)\r
- {\r
- mouseDragging = false;\r
-\r
- if(stretchGroup==null)\r
- return;\r
-\r
- if(stretchGroup.cs instanceof ClustalxColourScheme)\r
- {\r
- stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());\r
- repaint();\r
- }\r
-\r
- else if(stretchGroup.cs instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;\r
- stretchGroup.cs = ccs;\r
- SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;\r
-\r
- repaint();\r
- }\r
- else\r
- {\r
- if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())\r
- {\r
- ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs;\r
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\r
- }\r
-\r
- }\r
-\r
-\r
- changeEndRes = false;\r
- changeStartRes = false;\r
- stretchGroup = null;\r
- ap.idPanel.repaint();\r
- }\r
-\r
-\r
- boolean remove = false;\r
- public void doMouseDraggedDefineMode(MouseEvent evt)\r
- {\r
- int res = evt.getX()/av.getCharWidth() + av.getStartRes();\r
- int y = evt.getY()/av.getCharHeight() + av.getStartSeq();\r
-\r
- if(stretchGroup==null)\r
- return;\r
-\r
- if(res>av.alignment.getWidth())\r
- res = av.alignment.getWidth()-1;\r
-\r
-\r
- if(stretchGroup.getEndRes()==res)\r
- // Edit end res position of selected group\r
- changeEndRes = true;\r
-\r
- else if(stretchGroup.getStartRes()==res)\r
- // Edit start res position of selected group\r
- changeStartRes = true;\r
-\r
-\r
- if(res<av.getStartRes())\r
- res = av.getStartRes();\r
- else if(res>av.getEndRes())\r
- res = av.getEndRes();\r
-\r
- if(changeEndRes)\r
- {\r
- if(res>stretchGroup.getStartRes()-1)\r
- stretchGroup.setEndRes( res );\r
- }\r
- else if(changeStartRes)\r
- {\r
- if(res<stretchGroup.getEndRes()+1)\r
- stretchGroup.setStartRes( res );\r
- }\r
-\r
- int dragDirection = 0;\r
- if (y > oldSeq)\r
- dragDirection = 1;\r
- else if (y < oldSeq)\r
- dragDirection = -1;\r
-\r
- while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())\r
- {\r
- // This routine ensures we don't skip any sequences, as the\r
- // selection is quite slow.\r
- Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
-\r
- oldSeq += dragDirection;\r
- Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);\r
-\r
- if (stretchGroup.sequences.contains(nextSeq))\r
- {\r
- stretchGroup.deleteSequence(seq);\r
- stretchGroup.deleteSequence(nextSeq);\r
- }\r
- else\r
- {\r
- if(seq!=null)\r
- stretchGroup.addSequence(seq);\r
- stretchGroup.addSequence(nextSeq);\r
- }\r
- }\r
- oldSeq = y;\r
- mouseDragging = true;\r
- if(scrollThread!=null)\r
- scrollThread.setEvent(evt);\r
-\r
- repaint();\r
- }\r
-\r
- public void doMouseEnteredDefineMode(MouseEvent e)\r
- {\r
- if (scrollThread != null)\r
- scrollThread.running = false;\r
- }\r
-\r
- public void doMouseExitedDefineMode(MouseEvent e)\r
- {\r
- if (av.getWrapAlignment())\r
- return;\r
-\r
- if(mouseDragging)\r
- scrollThread = new ScrollThread();\r
-\r
- }\r
- // this class allows scrolling off the bottom of the visible alignment\r
- class ScrollThread extends Thread\r
- {\r
- MouseEvent evt;\r
- boolean running = false;\r
- public ScrollThread()\r
- {\r
- start();\r
- }\r
-\r
- public void setEvent(MouseEvent e)\r
- {\r
- evt = e;\r
- }\r
-\r
- public void stopScrolling()\r
- {\r
- running = false;\r
- }\r
-\r
- public void run()\r
- {\r
- running = true;\r
- while (running)\r
- {\r
- if(evt!=null)\r
- {\r
-\r
- if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)\r
- running = ap.scrollUp(true);\r
-\r
- if (mouseDragging && evt.getY() >= getHeight() &&\r
- av.alignment.getHeight() > av.getEndSeq())\r
- running = ap.scrollUp(false);\r
-\r
- if (mouseDragging && evt.getX() < 0)\r
- running = ap.scrollRight(true);\r
-\r
- else if (mouseDragging && evt.getX() >= getWidth())\r
- running = ap.scrollRight(false);\r
- }\r
-\r
- try\r
- {\r
- Thread.sleep(75);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
- }\r
-}\r
-\r
-\r
-\r
-}\r
-\r
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.datamodel.*;
+
+import jalview.schemes.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import java.util.Vector;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SeqPanel extends JPanel implements MouseListener,
+ MouseMotionListener, MouseWheelListener
+
+{
+ /** DOCUMENT ME!! */
+ public SeqCanvas seqCanvas;
+
+ /** DOCUMENT ME!! */
+ public AlignmentPanel ap;
+ protected int lastres;
+ protected int startseq;
+ protected AlignViewport av;
+
+ // if character is inserted or deleted, we will need to recalculate the conservation
+ boolean seqEditOccurred = false;
+ 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;
+
+ /**
+ * 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();
+
+ 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 cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
+
+ wrappedBlock = y / cHeight;
+ wrappedBlock += av.getStartRes() / cwidth;
+
+ res = wrappedBlock * cwidth + x / av.getCharWidth();
+
+ }
+ else
+ {
+ res = (x / av.getCharWidth()) + av.getStartRes();
+ }
+
+ if(av.hasHiddenColumns)
+ res = av.getColumnSelection().adjustForHiddenColumns(res);
+
+ return res;
+
+ }
+
+ int findSeq(MouseEvent evt)
+ {
+ int seq = 0;
+ int y = evt.getY();
+
+ if (av.wrapAlignment)
+ {
+ int hgap = av.charHeight;
+ if (av.scaleAboveWrapped)
+ hgap += av.charHeight;
+
+ int cHeight = av.getAlignment().getHeight() * av.charHeight
+ + hgap + seqCanvas.getAnnotationHeight();
+
+ y -= hgap;
+
+ 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;
+ }
+
+ 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)
+ {
+ if (av.featuresDisplayed.containsKey(sf.getType()))
+ {
+ allFeatures.addElement(sf);
+ }
+ }
+ index++;
+ }
+ }
+ return allFeatures;
+ }
+
+ void endEditing()
+ {
+ startseq = -1;
+ lastres = -1;
+ seqEditOccurred = false;
+ editingSeqs = false;
+ groupEditing = false;
+ keyboardNo1 = null;
+ keyboardNo2 = 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;
+ scrollToVisible();
+ }
+
+ void scrollToVisible()
+ {
+ if (seqCanvas.cursorX < 0)
+ seqCanvas.cursorX = 0;
+ else if (seqCanvas.cursorX > av.alignment.getWidth() - 1)
+ seqCanvas.cursorX = av.alignment.getWidth() - 1;
+
+ if (seqCanvas.cursorY < 0)
+ seqCanvas.cursorY = 0;
+ else if (seqCanvas.cursorY > av.alignment.getHeight() - 1)
+ seqCanvas.cursorY = av.alignment.getHeight() - 1;
+
+
+ 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.startRes)
+ {
+ if (!ap.scrollRight(false))
+ break;
+ }
+ while (seqCanvas.cursorX > av.endRes)
+ {
+ if (!ap.scrollRight(true))
+ break;
+ }
+ }
+ }
+ setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY),
+ seqCanvas.cursorX, seqCanvas.cursorY);
+
+ seqCanvas.repaint();
+ }
+
+ 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(false); i++)
+ {
+ int index = av.alignment.findIndex( sg.getSequenceAt(i) );
+ if(index > max)
+ max = index;
+ if(index < min)
+ min = index;
+ }
+
+ max ++;
+
+ if(topLeft)
+ {
+ sg.setStartRes(seqCanvas.cursorX);
+ if(sg.getEndRes()<seqCanvas.cursorX)
+ sg.setEndRes(seqCanvas.cursorX);
+
+ min = seqCanvas.cursorY;
+ }
+ else
+ {
+ sg.setEndRes(seqCanvas.cursorX);
+ if(sg.getStartRes()>seqCanvas.cursorX)
+ sg.setStartRes(seqCanvas.cursorX);
+
+ max = seqCanvas.cursorY+1;
+ }
+
+ if(min>max)
+ {
+ // Only the user can do this
+ av.setSelectionGroup(null);
+ }
+ else
+ {
+ // Now add any sequences between min and max
+ sg.getSequences(false).clear();
+ for (int i = min; i < max; i++)
+ {
+ sg.addSequence(av.alignment.getSequenceAt(i), false);
+ }
+ }
+ }
+
+ if (av.getSelectionGroup() == null)
+ {
+ SequenceGroup sg = new SequenceGroup();
+ sg.setStartRes(seqCanvas.cursorX);
+ sg.setEndRes(seqCanvas.cursorX);
+ sg.addSequence(sequence, false);
+ av.setSelectionGroup(sg);
+ }
+
+
+ ap.repaint();
+ }
+
+ void insertGapAtCursor(boolean group)
+ {
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+ av.alignment, HistoryItem.EDIT));
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1));
+ editOccurred();
+ }
+
+ void deleteGapAtCursor(boolean group)
+ {
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+ av.alignment, HistoryItem.EDIT));
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1);
+ editSequence(false, seqCanvas.cursorX);
+ editOccurred();
+ }
+
+ void numberPressed(char value)
+ {
+ if(keyboardNo1==null)
+ keyboardNo1 = new StringBuffer();
+
+ if(keyboardNo2!=null)
+ keyboardNo2.append(value);
+ else
+ keyboardNo1.append(value);
+ }
+
+ 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)
+ {
+ doMouseReleasedDefineMode(evt);
+ return;
+ }
+
+ editOccurred();
+
+ ap.repaint();
+ }
+
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt DOCUMENT ME!
+ */
+ public void mousePressed(MouseEvent evt)
+ {
+ lastMousePress = evt.getPoint();
+
+ 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;
+ }
+ else
+ {
+ doMousePressedDefineMode(evt);
+ return;
+ }
+
+
+
+ int seq = findSeq(evt);
+ int res = findRes(evt);
+
+ if(seq<0 || res<0)
+ return;
+
+ ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+ av.alignment, HistoryItem.EDIT));
+
+ 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);
+ }
+
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+
+
+ if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
+ return;
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+ if (res > sequence.getLength())
+ {
+ return;
+ }
+
+ if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+ {
+ seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+ }
+
+ setStatusMessage(sequence, res, seq);
+
+ // use aa to see if the mouse pointer is on a
+ if (av.showSequenceFeatures)
+ {
+ SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
+ if(features!=null)
+ {
+ StringBuffer sbuffer = new StringBuffer("<html>");
+ StringBuffer seqSpecific = new StringBuffer();
+
+ for (int i = 0; i < features.length; i++)
+ {
+
+ if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
+ (features[i].getEnd() >= sequence.findPosition(res)))
+ {
+ if(av.featuresDisplayed==null
+ || !av.featuresDisplayed.containsKey(features[i].getType()))
+ continue;
+
+
+ if (features[i].getType().equals("disulfide bond"))
+ {
+ if (features[i].getBegin() == sequence.findPosition(res)
+ || features[i].getEnd() == sequence.findPosition(res))
+ {
+ if (sbuffer.length() > 6)
+ sbuffer.append("<br>");
+ sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
+ features[i].getEnd());
+ if (features[i].links != null)
+ sbuffer.append(" <img src=\"" + linkImageURL + "\">");
+ }
+ }
+ else
+ {
+ if (sbuffer.length() > 6)
+ sbuffer.append("<br>");
+
+ sbuffer.append(features[i].getType() + " " +
+ features[i].begin);
+ if (features[i].begin != features[i].end)
+ sbuffer.append(" " + features[i].end);
+
+ if (features[i].getDescription() != null
+ && !features[i].description.equals(features[i].getType()))
+ sbuffer.append("; " + features[i].getDescription());
+
+ if (features[i].getValue("status") != null)
+ {
+ sbuffer.append("; (" + features[i].getValue("status") + ")");
+ }
+ if (features[i].links != null)
+ sbuffer.append(" <img src=\"" + linkImageURL + "\">");
+
+ }
+ }
+ else if(features[i].begin==0 && features[i].end==0)
+ {
+ // seqSpecific.append(features[i].featureGroup+": "
+ // + features[i].getType()+" "
+ // +features[i].getDescription()+"<br>");
+
+ }
+ }
+
+ if(seqSpecific.length()>0)
+ seqSpecific.setLength(seqSpecific.length()-4);
+
+ sbuffer.append(seqSpecific);
+ sbuffer.append("</html>");
+ if(sbuffer.length()==13) // <html></html>
+ setToolTipText("");
+ else
+ setToolTipText(sbuffer.toString());
+ }
+ else
+ setToolTipText("");
+ }
+ }
+
+ 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(fontSize<1)
+ fontSize = 1;
+
+ 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--;
+ }
+ 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;
+ }
+
+ if (!editingSeqs)
+ {
+ doMouseDraggedDefineMode(evt);
+ 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 (!groupEditing && av.hasHiddenRows)
+ {
+ if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null)
+ {
+ groupEditing = true;
+ }
+ }
+
+ //No group, but the sequence may represent a group
+ if (groupEditing
+ && sg == null
+ && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null)
+ {
+ groupEditing = false;
+ }
+
+ SequenceI seq = av.alignment.getSequenceAt(startseq);
+ StringBuffer message = new StringBuffer();
+ if (groupEditing)
+ message.append("Edit group:");
+ else
+ message.append("Edit sequence: "+seq.getName());
+
+ if(insertGap)
+ message.append(" insert ");
+ else
+ message.append(" delete ");
+
+ message.append(Math.abs(startres-lastres)+" gaps.");
+ ap.alignFrame.statusBar.setText(message.toString());
+
+
+ //Are we editing within a selection group?
+ if (groupEditing
+ || (sg != null && sg.getSequences(true).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)
+ {
+ sg = new SequenceGroup(null, null, false, false, false, 0,
+ av.alignment.getWidth()-1);
+ sg.addSequence(av.alignment.getSequenceAt(startseq), false);
+ }
+
+ 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(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)
+ {
+ fixedLeft = y2;
+ }
+ else
+ {
+ fixedRight = y2 - 1;
+ }
+ }
+ }
+
+
+ if (groupEditing)
+ {
+ // 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
+ )
+ {
+ sg.setEndRes(av.alignment.getWidth() + startres - lastres);
+ fixedRight = sg.getEndRes();
+ }
+
+ // 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--)
+ {
+ blank = true;
+ for (int s = 0; s < sg.getSize(true); s++)
+ {
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);
+ for (int j = 0; j < startres - lastres; j++)
+ {
+ if (!jalview.util.Comparison.isGap(
+ seq.getCharAt(fixedRight - j)))
+ {
+ blank = false;
+ break;
+ }
+ }
+ }
+ if (blank)
+ break;
+ }
+
+ if (!blank)
+ {
+ if(sg.getSize(false) == av.alignment.getHeight() )
+ {
+ if((av.hasHiddenColumns
+ && startres<av.getColumnSelection().getHiddenBoundaryRight(startres)))
+ {
+ 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;
+ }
+ }
+ }
+
+
+ // drag to left
+ else if(!insertGap)
+ {
+ /// Are we able to delete?
+ // ie are all columns blank?
+
+ for (int s = 0; s < sg.getSize(true); s++)
+ {
+ seq = (SequenceI)sg.getSequences(true).elementAt(s);
+
+ for (int j = startres; 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
+ endEditing();
+ return;
+ }
+ }
+ }
+ }
+
+
+ for (int i = 0; i < sg.getSize(true); i++)
+ {
+ seq = (SequenceI) sg.getSequences(true).elementAt(i);
+
+ if (insertGap)
+ {
+ // dragging to the right
+ for (int j = lastres; j < startres; j++)
+ {
+ if (fixedColumns && fixedRight != -1)
+ {
+ insertChar(j, seq, fixedRight);
+ }
+ else
+ insertChar(j, seq);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ for (int j = lastres; j > startres; j--)
+ {
+ if (fixedColumns && fixedRight != -1)
+ {
+ deleteChar(startres, seq, fixedRight);
+ }
+ else
+ {
+ deleteChar(startres, seq);
+ }
+ }
+ }
+ }
+ }
+ else /////Editing a single sequence///////////
+ {
+ if (insertGap)
+ {
+ // dragging to the right
+ for (int j = lastres; j < startres; j++)
+ {
+ if (fixedColumns && fixedRight != -1)
+ {
+ insertChar(j, seq, fixedRight);
+ }
+ else
+ insertChar(j, seq);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ for (int j = lastres; j > startres; j--)
+ {
+ if (fixedColumns && fixedRight != -1)
+ {
+ deleteChar(startres, seq, fixedRight);
+ }
+ else
+ {
+ deleteChar(startres, seq);
+ }
+ }
+ }
+ }
+
+ lastres = startres;
+ seqCanvas.repaint();
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param j DOCUMENT ME!
+ * @param seq DOCUMENT ME!
+ */
+ void insertChar(int j, SequenceI seq)
+ {
+ seq.insertCharAt(j, av.getGapCharacter());
+ seqEditOccurred = true;
+ }
+
+ void insertChar(int j, SequenceI seq, int fixedColumn)
+ {
+ //Find the next gap before the end of the visible region boundary
+ //If lastCol > j, theres a boundary after the gap insertion
+ int blankColumn = fixedColumn;
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
+ {
+ //Theres a space, so break and insert the gap
+ break;
+ }
+ }
+
+ if (blankColumn <= j)
+ {
+ blankColumn = fixedColumn;
+ endEditing();
+ return;
+ }
+
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn)))
+ {
+ //Just Checking
+ System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn));
+ return;
+ }
+
+ seq.deleteCharAt(blankColumn);
+ seq.insertCharAt(j, av.getGapCharacter());
+ seqEditOccurred = true;
+ }
+
+ void deleteChar(int j, SequenceI seq, int fixedColumn)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+ {
+ ap.alignFrame.statusBar.setText(
+ "End editing: Tried removing residue " + seq.getCharAt(j));
+ return;
+ }
+
+ seq.deleteCharAt(j);
+ seq.insertCharAt(fixedColumn, av.getGapCharacter());
+ seqEditOccurred = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param j DOCUMENT ME!
+ * @param seq DOCUMENT ME!
+ */
+ void deleteChar(int j, SequenceI seq)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(j)))
+ {
+ ap.alignFrame.statusBar.setText(
+ "End editing: Tried removing residue " + seq.getCharAt(j));
+ return;
+ }
+
+ seq.deleteCharAt(j);
+ seqEditOccurred = true;
+ seqCanvas.repaint();
+ }
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent e)
+ {
+ if(oldSeq < 0)
+ 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)
+ {}
+
+ 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 i DOCUMENT ME!
+ */
+ void editOccurred()
+ {
+ if (!seqEditOccurred)
+ {
+ ap.alignFrame.historyList.pop();
+ ap.alignFrame.updateEditMenuBar();
+ }
+
+ endEditing();
+
+ av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
+
+ }
+
+ /**
+ * 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;
+ }
+
+ 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(false).contains(sequence) ||
+ (stretchGroup.getStartRes() > res) ||
+ (stretchGroup.getEndRes() < res))
+ {
+ stretchGroup = null;
+
+ SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence);
+
+ if (allGroups != null)
+ {
+ for (int i = 0; i < allGroups.length; i++)
+ {
+ if ((allGroups[i].getStartRes() <= res) &&
+ (allGroups[i].getEndRes() >= res))
+ {
+ stretchGroup = allGroups[i];
+ break;
+ }
+ }
+ }
+
+ av.setSelectionGroup(stretchGroup);
+
+ }
+
+
+ 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)
+ {
+ 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(true),
+ stretchGroup.getWidth());
+ }
+
+ if (stretchGroup.cs.conservationApplied())
+ {
+ SliderPanel.setConservationSlider(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ stretchGroup.recalcConservation();
+ }
+ else
+ {
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ }
+ }
+ changeEndRes = false;
+ changeStartRes = false;
+ stretchGroup = null;
+ PaintRefresher.Refresh(av.alignment);
+ }
+
+ /**
+ * 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);
+ }
+ }
+
+ int dragDirection = 0;
+
+ if (y > oldSeq)
+ {
+ 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;
+
+ Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
+
+ if (stretchGroup.getSequences(false).contains(nextSeq))
+ {
+ stretchGroup.deleteSequence(seq, false);
+ }
+ else
+ {
+ if (seq != null)
+ {
+ stretchGroup.addSequence(seq, false);
+ }
+
+ 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)
+ {
+ 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);
+ }
+ }
+
+ try
+ {
+ Thread.sleep(20);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff