-package jalview.appletgui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import jalview.datamodel.*;\r
-import java.util.*;\r
-import jalview.schemes.*;\r
-\r
-\r
-public class SeqPanel extends Panel\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);\r
-\r
- ap = p;\r
-\r
- seqCanvas.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
- seqCanvas.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
- seqCanvas.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)*(getSize().width/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
-\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
- seqCanvas.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
- seqCanvas.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
- seqCanvas.repaint();\r
- seqEditOccurred=seq;\r
- }\r
-\r
-\r
- void updateConservation(int i)\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( ( evt.getModifiers() & InputEvent .BUTTON3_MASK ) == InputEvent.BUTTON3_MASK )\r
- {\r
- APopupMenu popup = new APopupMenu(ap, null);\r
- this.add(popup);\r
- popup.show(this, evt.getX(), evt.getY());\r
- }\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
-\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
- seqCanvas.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
- seqCanvas.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.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
- seqCanvas.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() >= getSize().height &&\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() >= getSize().width)\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 (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.commands.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.SequenceListener;
+import jalview.structure.StructureSelectionManager;
+
+public class SeqPanel extends Panel implements MouseMotionListener,
+ MouseListener, SequenceListener
+{
+
+ public SeqCanvas seqCanvas;
+
+ 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;
+
+ int oldSeq = -1;
+
+ boolean changeEndSeq = false;
+
+ boolean changeStartSeq = false;
+
+ boolean changeEndRes = false;
+
+ boolean changeStartRes = false;
+
+ SequenceGroup stretchGroup = null;
+
+ StringBuffer keyboardNo1;
+
+ StringBuffer keyboardNo2;
+
+ boolean mouseWheelPressed = false;
+
+ Point lastMousePress;
+
+ EditCommand editCommand;
+
+ StructureSelectionManager ssm;
+
+ public SeqPanel(AlignViewport avp, AlignmentPanel p)
+ {
+ this.av = avp;
+
+ seqCanvas = new SeqCanvas(avp);
+ setLayout(new BorderLayout());
+ add(seqCanvas);
+
+ ap = p;
+
+ seqCanvas.addMouseMotionListener(this);
+ seqCanvas.addMouseListener(this);
+ ssm = StructureSelectionManager.getStructureSelectionManager(av.applet);
+ ssm.addStructureViewerListener(this);
+
+ seqCanvas.repaint();
+ }
+
+ void endEditing()
+ {
+ if (editCommand != null && editCommand.getSize() > 0)
+ {
+ ap.alignFrame.addHistoryItem(editCommand);
+ av.firePropertyChange("alignment", null, av.getAlignment()
+ .getSequences());
+ }
+
+ startseq = -1;
+ lastres = -1;
+ editingSeqs = false;
+ groupEditing = false;
+ keyboardNo1 = null;
+ keyboardNo2 = null;
+ editCommand = null;
+ }
+
+ void setCursorRow()
+ {
+ seqCanvas.cursorY = getKeyboardNo1() - 1;
+ scrollToVisible();
+ }
+
+ void setCursorColumn()
+ {
+ seqCanvas.cursorX = getKeyboardNo1() - 1;
+ scrollToVisible();
+ }
+
+ void setCursorRowAndColumn()
+ {
+ if (keyboardNo2 == null)
+ {
+ keyboardNo2 = new StringBuffer();
+ }
+ else
+ {
+ seqCanvas.cursorX = getKeyboardNo1() - 1;
+ seqCanvas.cursorY = getKeyboardNo2() - 1;
+ scrollToVisible();
+ }
+ }
+
+ void setCursorPosition()
+ {
+ SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(
+ seqCanvas.cursorY);
+
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 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();
+
+ while (!av.colSel.isVisible(seqCanvas.cursorX)
+ && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+ {
+ seqCanvas.cursorX += dx;
+ }
+
+ if (seqCanvas.cursorX >= maxWidth
+ || !av.colSel.isVisible(seqCanvas.cursorX))
+ {
+ seqCanvas.cursorX = original;
+ }
+ }
+ 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);
+ }
+ while (seqCanvas.cursorX < av.colSel
+ .adjustForHiddenColumns(av.startRes))
+ {
+
+ if (!ap.scrollRight(false))
+ {
+ break;
+ }
+ }
+ while (seqCanvas.cursorX > av.colSel
+ .adjustForHiddenColumns(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(); 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(null).removeAllElements();
+ 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.paintAlignment(false);
+ av.sendSelection();
+ }
+
+ void insertGapAtCursor(boolean group)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(true, seqCanvas.cursorX + getKeyboardNo1());
+ endEditing();
+ }
+
+ void deleteGapAtCursor(boolean group)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX + getKeyboardNo1();
+ editSequence(false, seqCanvas.cursorX);
+ endEditing();
+ }
+
+ void numberPressed(char value)
+ {
+ if (keyboardNo1 == null)
+ {
+ keyboardNo1 = new StringBuffer();
+ }
+
+ if (keyboardNo2 != null)
+ {
+ keyboardNo2.append(value);
+ }
+ else
+ {
+ keyboardNo1.append(value);
+ }
+ }
+
+ int getKeyboardNo1()
+ {
+ if (keyboardNo1 == null)
+ return 1;
+ else
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
+ }
+
+ int getKeyboardNo2()
+ {
+ if (keyboardNo2 == null)
+ return 1;
+ else
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
+ }
+
+ 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());
+
+ }
+
+ public void mousePressed(MouseEvent evt)
+ {
+ lastMousePress = evt.getPoint();
+
+ // For now, ignore the mouseWheel font resizing on Macs
+ // As the Button2_mask always seems to be true
+ if ((evt.getModifiers() & InputEvent.BUTTON2_MASK) == InputEvent.BUTTON2_MASK
+ && !av.MAC)
+ {
+ mouseWheelPressed = true;
+ return;
+ }
+
+ if (evt.isShiftDown() || evt.isControlDown() || evt.isAltDown())
+ {
+ if (evt.isControlDown() || evt.isAltDown())
+ {
+ groupEditing = true;
+ }
+ editingSeqs = true;
+ }
+ else
+ {
+ doMousePressedDefineMode(evt);
+ return;
+ }
+
+ int seq = findSeq(evt);
+ int res = findRes(evt);
+
+ if (seq < 0 || res < 0)
+ {
+ return;
+ }
+
+ if ((seq < av.getAlignment().getHeight())
+ && (res < av.getAlignment().getSequenceAt(seq).getLength()))
+ {
+ startseq = seq;
+ lastres = res;
+ }
+ else
+ {
+ startseq = -1;
+ lastres = -1;
+ }
+
+ return;
+ }
+
+ 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,
+ 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 mouseReleased(MouseEvent evt)
+ {
+ mouseDragging = false;
+ mouseWheelPressed = false;
+ ap.paintAlignment(true);
+
+ if (!editingSeqs)
+ {
+ doMouseReleasedDefineMode(evt);
+ return;
+ }
+
+ endEditing();
+
+ }
+
+ 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(getSize().width);
+ if (cwidth < 1)
+ {
+ return 0;
+ }
+
+ 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)
+ {
+ final int sqnum = findAlRow(evt);
+ return (sqnum < 0) ? 0 : sqnum;
+ }
+
+ /**
+ *
+ * @param evt
+ * @return row in alignment that was selected (or -1 for column selection)
+ */
+ private int findAlRow(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);
+ if (seq < 0)
+ {
+ seq = -1;
+ }
+ }
+ else
+ {
+ seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(),
+ av.alignment.getHeight() - 1);
+ if (seq < 0)
+ {
+ seq = -1;
+ }
+ }
+
+ return seq;
+ }
+
+ public void doMousePressed(MouseEvent evt)
+ {
+
+ int seq = findSeq(evt);
+ int res = findRes(evt);
+
+ if (seq < av.getAlignment().getHeight()
+ && res < av.getAlignment().getSequenceAt(seq).getLength())
+ {
+ // char resstr = align.getSequenceAt(seq).getSequence().charAt(res);
+ // Find the residue's position in the sequence (res is the position
+ // in the alignment
+
+ startseq = seq;
+ lastres = res;
+ }
+ else
+ {
+ startseq = -1;
+ lastres = -1;
+ }
+
+ return;
+ }
+
+ String lastMessage;
+
+ public void mouseOverSequence(SequenceI sequence, int index, int pos)
+ {
+ String tmp = sequence.hashCode() + index + "";
+ if (lastMessage == null || !lastMessage.equals(tmp))
+ ssm.mouseOverSequence(sequence, index, pos, av);
+
+ lastMessage = tmp;
+ }
+
+ public void highlightSequence(SearchResults results)
+ {
+ if (av.followHighlight)
+ {
+ if (ap.scrollToPosition(results, true))
+ {
+ ap.alignFrame.repaint();
+ }
+ }
+ seqCanvas.highlightSearchResults(results);
+
+ }
+
+ public void updateColours(SequenceI seq, int index)
+ {
+ System.out.println("update the seqPanel colours");
+ // repaint();
+ }
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+
+ if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0)
+ {
+ if (tooltip != null)
+ {
+ tooltip.setTip("");
+ }
+ return;
+ }
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ if (res > sequence.getLength())
+ {
+ if (tooltip != null)
+ {
+ tooltip.setTip("");
+ }
+ return;
+ }
+
+ int respos = sequence.findPosition(res);
+ if (ssm != null)
+ mouseOverSequence(sequence, res, respos);
+
+ 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 + " (" + respos + ")");
+ }
+ }
+
+ ap.alignFrame.statusBar.setText(text.toString());
+
+ StringBuffer tooltipText = new StringBuffer();
+ 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)
+ {
+ 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());
+ }
+ tooltipText.append("\n");
+ }
+ }
+ }
+
+ // use aa to see if the mouse pointer is on a
+ SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+ sequence.findPosition(res));
+
+ int index = 0;
+ while (index < allFeatures.length)
+ {
+ SequenceFeature sf = allFeatures[index];
+
+ tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end);
+
+ if (sf.getDescription() != null)
+ {
+ tooltipText.append(" " + sf.getDescription());
+ }
+
+ if (sf.getValue("status") != null)
+ {
+ String status = sf.getValue("status").toString();
+ if (status.length() > 0)
+ {
+ tooltipText.append(" (" + sf.getValue("status") + ")");
+ }
+ }
+ tooltipText.append("\n");
+
+ index++;
+ }
+
+ if (tooltip == null)
+ {
+ tooltip = new Tooltip(tooltipText.toString(), seqCanvas);
+ }
+ else
+ {
+ tooltip.setTip(tooltipText.toString());
+ }
+ }
+
+ SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res)
+ {
+ Vector tmp = new Vector();
+ SequenceFeature[] features = sequence.getSequenceFeatures();
+ if (features != null)
+ {
+ for (int i = 0; i < features.length; i++)
+ {
+ if (av.featuresDisplayed == null
+ || !av.featuresDisplayed.containsKey(features[i].getType()))
+ {
+ continue;
+ }
+
+ if (features[i].featureGroup != null
+ && seqCanvas.fr.featureGroups != null
+ && seqCanvas.fr.featureGroups
+ .containsKey(features[i].featureGroup)
+ && !((Boolean) seqCanvas.fr.featureGroups
+ .get(features[i].featureGroup)).booleanValue())
+ continue;
+
+ if ((features[i].getBegin() <= res)
+ && (features[i].getEnd() >= res))
+ {
+ tmp.addElement(features[i]);
+ }
+ }
+ }
+
+ features = new SequenceFeature[tmp.size()];
+ tmp.copyInto(features);
+
+ return features;
+ }
+
+ Tooltip tooltip;
+
+ 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.y) > Math.abs(evt.getX()
+ - lastMousePress.x))
+ {
+ int fontSize = av.font.getSize();
+
+ if (evt.getY() < lastMousePress.y && av.charHeight > 1)
+ {
+ fontSize--;
+ }
+ else if (evt.getY() > lastMousePress.y)
+ {
+ fontSize++;
+ }
+
+ if (fontSize < 1)
+ {
+ fontSize = 1;
+ }
+
+ av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+ av.charWidth = oldWidth;
+ }
+ else
+ {
+ if (evt.getX() < lastMousePress.x && av.charWidth > 1)
+ {
+ av.charWidth--;
+ }
+ else if (evt.getX() > lastMousePress.x)
+ {
+ av.charWidth++;
+ }
+
+ if (av.charWidth < 1)
+ {
+ av.charWidth = 1;
+ }
+ }
+
+ ap.fontChanged();
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+ av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+
+ lastMousePress = evt.getPoint();
+
+ ap.paintAlignment(false);
+ ap.annotationPanel.image = null;
+ 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();
+
+ SequenceI seq = av.alignment.getSequenceAt(startseq);
+
+ if (!groupEditing && av.hasHiddenRows)
+ {
+ if (av.hiddenRepSequences != null
+ && av.hiddenRepSequences.containsKey(seq))
+ {
+ 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());
+
+ // 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))
+ {
+ 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 (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)
+ {
+ 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)
+ {
+ 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 (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 (!blank)
+ {
+ if (sg.getSize() == 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 (g = 0; g < groupSize; g++)
+ {
+ for (int j = startres; j < lastres; j++)
+ {
+ if (groupSeqs[g].getLength() <= j)
+ {
+ continue;
+ }
+
+ if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j)))
+ {
+ // Not a gap, block edit not valid
+ endEditing();
+ return;
+ }
+ }
+ }
+ }
+
+ if (insertGap)
+ {
+ // dragging to the right
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j < startres; j++)
+ {
+ insertChar(j, groupSeqs, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs,
+ startres, startres - lastres, av.alignment, true);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j > startres; j--)
+ {
+ deleteChar(startres, groupSeqs, fixedRight);
+ }
+ }
+ else
+ {
+ editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs,
+ startres, lastres - startres, av.alignment, true);
+ }
+
+ }
+ }
+ 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)))
+ {
+ endEditing();
+ break;
+ }
+ deleteChar(startres, new SequenceI[]
+ { seq }, fixedRight);
+ }
+ }
+ else
+ {
+ // could be a keyboard edit trying to delete none gaps
+ int max = 0;
+ for (int m = startres; m < lastres; m++)
+ {
+ if (!jalview.util.Comparison.isGap(seq.getCharAt(m)))
+ {
+ break;
+ }
+ max++;
+ }
+
+ if (max > 0)
+ {
+ editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[]
+ { seq }, startres, max, av.alignment, true);
+ }
+ }
+ }
+ }
+
+ lastres = startres;
+ seqCanvas.repaint();
+ }
+
+ 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
+
+ for (blankColumn = fixedColumn; blankColumn > j; blankColumn--)
+ {
+ if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn)))
+ {
+ // Theres a space, so break and insert the gap
+ break;
+ }
+ }
+
+ if (blankColumn <= j)
+ {
+ blankColumn = fixedColumn;
+ endEditing();
+ return;
+ }
+ }
+
+ 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);
+ }
+
+ // ////////////////////////////////////////
+ // ///Everything below this is for defining the boundary of the rubberband
+ // ////////////////////////////////////////
+ public void doMousePressedDefineMode(MouseEvent evt)
+ {
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+
+ int res = findRes(evt);
+ int seq = findSeq(evt);
+ oldSeq = seq;
+ startWrapBlock = wrappedBlock;
+
+ if (seq == -1)
+ {
+ 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)
+ {
+ 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);
+ }
+
+ // DETECT RIGHT MOUSE BUTTON IN AWT
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ {
+ SequenceFeature[] allFeatures = findFeaturesAtRes(sequence,
+ sequence.findPosition(res));
+
+ Vector links = null;
+ if (allFeatures != null)
+ {
+ for (int i = 0; i < allFeatures.length; i++)
+ {
+ if (allFeatures[i].links != null)
+ {
+ if (links == null)
+ {
+ links = new Vector();
+ }
+ for (int j = 0; j < allFeatures[i].links.size(); j++)
+ {
+ links.addElement(allFeatures[i].links.elementAt(j));
+ }
+ }
+ }
+ }
+ APopupMenu popup = new APopupMenu(ap, null, links);
+ this.add(popup);
+ popup.show(this, evt.getX(), evt.getY());
+ return;
+ }
+
+ if (av.cursorMode)
+ {
+ seqCanvas.cursorX = findRes(evt);
+ seqCanvas.cursorY = findSeq(evt);
+ seqCanvas.repaint();
+ return;
+ }
+
+ // Only if left mouse button do we want to change group sizes
+
+ 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;
+
+ if (av.getConservationSelected())
+ {
+ SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+ "Background");
+ }
+ if (av.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+ "Background");
+ }
+
+ }
+ }
+
+ 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());
+ stretchGroup.recalcConservation();
+ }
+ else
+ {
+ SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
+ stretchGroup.getName());
+ }
+ }
+ changeEndRes = false;
+ changeStartRes = false;
+ stretchGroup = null;
+ PaintRefresher.Refresh(ap, av.getSequenceSetId());
+ ap.paintAlignment(true);
+ av.sendSelection();
+ }
+
+ public void doMouseDraggedDefineMode(MouseEvent evt)
+ {
+ int res = findRes(evt);
+ int y = findSeq(evt);
+
+ if (wrappedBlock != startWrapBlock)
+ {
+ return;
+ }
+
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ mouseDragging = true;
+
+ if (y > av.alignment.getHeight())
+ {
+ y = av.alignment.getHeight() - 1;
+ }
+
+ 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 < 0)
+ {
+ res = 0;
+ }
+
+ 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(null).contains(nextSeq))
+ {
+ stretchGroup.deleteSequence(seq, false);
+ }
+ else
+ {
+ if (seq != null)
+ {
+ stretchGroup.addSequence(seq, false);
+ }
+
+ stretchGroup.addSequence(nextSeq, false);
+ }
+ }
+
+ if (oldSeq < 0)
+ {
+ oldSeq = -1;
+ }
+
+ if (res > av.endRes || res < av.startRes || y < av.startSeq
+ || y > av.endSeq)
+ {
+ mouseExited(evt);
+ }
+
+ if (scrollThread != null)
+ {
+ scrollThread.setEvent(evt);
+ }
+
+ seqCanvas.repaint();
+ }
+
+ public void mouseEntered(MouseEvent e)
+ {
+ if (oldSeq < 0)
+ {
+ oldSeq = 0;
+ }
+
+ if (scrollThread != null)
+ {
+ scrollThread.running = false;
+ scrollThread = null;
+ }
+ }
+
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging && scrollThread == null)
+ {
+ scrollThread = new ScrollThread();
+ }
+ }
+
+ 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() >= getSize().height
+ && av.alignment.getHeight() > av.getEndSeq())
+ {
+ running = ap.scrollUp(false);
+ }
+
+ if (mouseDragging && evt.getX() < 0)
+ {
+ running = ap.scrollRight(false);
+ }
+
+ else if (mouseDragging && evt.getX() >= getSize().width)
+ {
+ running = ap.scrollRight(true);
+ }
+ }
+
+ try
+ {
+ Thread.sleep(75);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ }
+
+ /**
+ * modify current selection according to a received message.
+ */
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ SelectionSource source)
+ {
+ // TODO: fix this hack - source of messages is align viewport, but SeqPanel
+ // handles selection messages...
+ // TODO: extend config options to allow user to control if selections may be
+ // shared between viewports.
+ if (av != null
+ && (av == source || !av.followSelection || (source instanceof AlignViewport && ((AlignViewport) source)
+ .getSequenceSetId().equals(av.getSequenceSetId()))))
+ {
+ return;
+ }
+ // do we want to thread this ? (contention with seqsel and colsel locks, I
+ // suspect)
+ // rules are: colsel is copied if there is a real intersection between
+ // sequence selection
+ boolean repaint = false, copycolsel = true;
+ if (av.selectionGroup == null || !av.isSelectionGroupChanged())
+ {
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize()>0)
+ {
+ if (av.alignment == null)
+ {
+ System.out
+ .println("Selection message: alignviewport av SeqSetId="
+ + av.getSequenceSetId() + " ViewId="
+ + av.getViewId()
+ + " 's alignment is NULL! returning immediatly.");
+ return;
+ }
+ sgroup = seqsel.intersect(av.alignment,
+ (av.hasHiddenRows) ? av.hiddenRepSequences : null);
+ if ((sgroup == null || sgroup.getSize() == 0)
+ && (colsel == null || colsel.size() == 0))
+ {
+ // don't copy columns if the region didn't intersect.
+ copycolsel = false;
+ }
+ }
+ if (sgroup != null && sgroup.getSize() > 0)
+ {
+ av.setSelectionGroup(sgroup);
+ }
+ else
+ {
+ av.setSelectionGroup(null);
+ }
+ repaint = av.isSelectionGroupChanged();
+ }
+ if (copycolsel && (av.colSel == null || !av.isColSelChanged()))
+ {
+ // the current selection is unset or from a previous message
+ // so import the new colsel.
+ if (colsel == null || colsel.size() == 0)
+ {
+ if (av.colSel != null)
+ {
+ av.colSel.clear();
+ }
+ }
+ else
+ {
+ // TODO: shift colSel according to the intersecting sequences
+ if (av.colSel == null)
+ {
+ av.colSel = new ColumnSelection(colsel);
+ }
+ else
+ {
+ av.colSel.setElementsFrom(colsel);
+ }
+ }
+ repaint |= av.isColSelChanged();
+ }
+ if (copycolsel && av.hasHiddenColumns
+ && (av.colSel == null || av.colSel.getHiddenColumns() == null))
+ {
+ System.err.println("Bad things");
+ }
+ if (repaint)
+ {
+ ap.scalePanelHolder.repaint();
+ ap.repaint();
+ }
+ }
+
+ /**
+ * scroll to the given row/column - or nearest visible location
+ * @param row
+ * @param column
+ */
+ public void scrollTo(int row, int column)
+ {
+
+ row = row<0 ? ap.av.startSeq : row;
+ column = column<0 ? ap.av.startRes : column;
+ ap.scrollTo(row, row, column, true, true);
+ }
+ /**
+ * scroll to the given row - or nearest visible location
+ * @param row
+ */
+ public void scrollToRow(int row)
+ {
+
+ row = row<0 ? ap.av.startSeq : row;
+ ap.scrollTo(row, row, ap.av.startRes, true, true);
+ }
+ /**
+ * scroll to the given column - or nearest visible location
+ * @param column
+ */
+ public void scrollToColumn(int column)
+ {
+
+ column = column<0 ? ap.av.startRes : column;
+ ap.scrollTo(ap.av.startRes, ap.av.startRes, column, true, true);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff