-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
-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
-import jalview.analysis.Conservation;\r
-\r
-public class SeqPanel extends JPanel\r
-{\r
-\r
- public SeqCanvas seqCanvas;\r
- public AlignmentPanel ap;\r
-\r
- protected int lastres;\r
- protected int startseq;\r
- int startEdit=-1;\r
- int endEdit=-1;\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
- boolean editingSeqs = false;\r
- boolean groupEditing = 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( editingSeqs )\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(editingSeqs)\r
- doMouseReleased(evt);\r
- else\r
- doMouseReleasedDefineMode(evt);\r
-\r
- }\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if(av.getWrapAlignment())\r
- return;\r
- if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())\r
- {\r
- if(evt.isAltDown() || evt.isControlDown())\r
- groupEditing = true;\r
-\r
- editingSeqs = true;\r
- doMousePressed(evt);\r
- }\r
- else\r
- doMousePressedDefineMode(evt);\r
- }\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment() || editingSeqs)\r
- return;\r
- doMouseExitedDefineMode(evt);\r
-\r
- }\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- if (av.getWrapAlignment() || editingSeqs)\r
- return;\r
- doMouseEnteredDefineMode(evt);\r
- }\r
-\r
- });\r
- repaint();\r
- }\r
-\r
-\r
- public void doMouseReleased(MouseEvent evt) {\r
-\r
- if(seqEditOccurred>-1)\r
- editOccurred(seqEditOccurred);\r
-\r
- startseq = -1;\r
- lastres = -1;\r
- seqEditOccurred = -1;\r
- editingSeqs = false;\r
- groupEditing = false;\r
-\r
- ap.repaint();\r
- }\r
-\r
- public void doMousePressed(MouseEvent evt) {\r
-\r
- ap.alignFrame.addHistoryItem( new HistoryItem(\r
- "Edit Sequence",av.alignment, HistoryItem.EDIT));\r
-\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
- startseq = seq;\r
- lastres = res;\r
- }\r
- else\r
- {\r
- startseq = -1;\r
- lastres = -1;\r
- }\r
-\r
- startEdit = lastres;\r
- endEdit = lastres;\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
-\r
- // If we're dragging we're editing\r
- int res = evt.getX() / av.getCharWidth() + av.getStartRes();\r
- if (res < 0)\r
- res = 0;\r
-\r
- if (lastres == -1 || lastres == res)\r
- return;\r
-\r
- boolean dragRight = true;\r
- if (res < av.getAlignment().getWidth() && res < lastres)\r
- dragRight = false;\r
-\r
-\r
- if (res != lastres)\r
- {\r
- // Group editing\r
- if (groupEditing)\r
- {\r
- SequenceGroup sg = av.getSelectionGroup();\r
- if(sg==null)\r
- {\r
- lastres=-1;\r
- return;\r
- }\r
-\r
- // drag to right\r
- if(dragRight)\r
- sg.setEndRes(sg.getEndRes() + (res-lastres));\r
-\r
- // drag to left\r
- else\r
- {\r
- /// Are we able to delete?\r
- // ie are all columns blank?\r
- boolean deleteAllowed = false;\r
- for (int s = 0; s < sg.getSize(); s++)\r
- {\r
- SequenceI seq = sg.getSequenceAt(s);\r
- for (int j=res; j<lastres; j++)\r
- {\r
- if(seq.getSequence().length()<=j)\r
- continue;\r
-\r
- if(!jalview.util.Comparison.isGap(seq.getSequence().charAt(j)))\r
- {\r
- // Not a gap, block edit not valid\r
- res=j+1;\r
- deleteAllowed = false;\r
- continue;\r
- }\r
- deleteAllowed = true;\r
- }\r
- }\r
-\r
- if(!deleteAllowed)\r
- {\r
- lastres = -1;\r
- return;\r
- }\r
-\r
- sg.setEndRes(sg.getEndRes() - (lastres-res));\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 (dragRight)\r
- for (int j = lastres; j < res; j++)\r
- insertChar(j, k);\r
-\r
- // drag to left\r
- else\r
- {\r
- for (int j = res; j < lastres; j++)\r
- {\r
- if(s.getLength()>j)\r
- deleteChar(res, k);\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 = lastres; j > res; j--)\r
- {\r
- if( jalview.util.Comparison.isGap(\r
- av.alignment.getSequenceAt(startseq).getSequence().charAt(res)))\r
-\r
- deleteChar(res, startseq);\r
- else\r
- {\r
-\r
- break;\r
- }\r
- }\r
- }\r
-\r
- }\r
- }\r
-\r
- endEdit = res;\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
- av.alignment.getSequenceAt(seq).deleteCharAt(j);\r
- seqEditOccurred=seq;\r
-\r
- av.alignment.getWidth();\r
- repaint();\r
- }\r
-\r
-\r
- void editOccurred(int i)\r
- {\r
- if(endEdit==startEdit)\r
- {\r
- ap.alignFrame.historyList.pop();\r
- ap.alignFrame.updateEditMenuBar();\r
- }\r
-\r
- av.updateConservation();\r
- av.updateConsensus();\r
-\r
- // Y O Y CLUSTALX\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme)\r
- {\r
- ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
- if(ccs.cs instanceof ClustalxColourScheme)\r
- {\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- av.alignment.getSequences(), 0,\r
- av.alignment.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, av.ConsPercGaps);\r
-\r
- ClustalxColourScheme cxs = (ClustalxColourScheme)ccs.cs;\r
- cxs.resetClustalX(av.alignment.getSequences(), av.alignment.getWidth());\r
- ccs = new ConservationColourScheme(c, cxs);\r
- av.setGlobalColourScheme(ccs);\r
- }\r
- }\r
-\r
- if(cs instanceof ClustalxColourScheme)\r
- {\r
- ((ClustalxColourScheme)cs).resetClustalX(av.alignment.getSequences(),\r
- av.alignment.getWidth());\r
- av.setGlobalColourScheme(cs);\r
- }\r
-\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
- stretchGroup.getWidth();\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
- SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());\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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.api.AlignViewportI;
+import jalview.bin.Cache;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.commands.EditCommand.Edit;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.SequenceAnnotationReport;
+import jalview.renderer.ResidueShaderI;
+import jalview.schemes.ResidueProperties;
+import jalview.structure.SelectionListener;
+import jalview.structure.SelectionSource;
+import jalview.structure.SequenceListener;
+import jalview.structure.StructureSelectionManager;
+import jalview.structure.VamsasSource;
+import jalview.util.Comparison;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision: 1.130 $
+ */
+public class SeqPanel extends JPanel
+ implements MouseListener, MouseMotionListener, MouseWheelListener,
+ SequenceListener, SelectionListener
+
+{
+ /** DOCUMENT ME!! */
+ public SeqCanvas seqCanvas;
+
+ /** DOCUMENT ME!! */
+ public AlignmentPanel ap;
+
+ /*
+ * last column position for mouseMoved event
+ */
+ private int lastMouseColumn;
+
+ /*
+ * last sequence offset for mouseMoved event
+ */
+ private int lastMouseSeq;
+
+ protected int lastres;
+
+ protected int startseq;
+
+ protected AlignViewport av;
+
+ ScrollThread scrollThread = null;
+
+ boolean mouseDragging = false;
+
+ boolean editingSeqs = false;
+
+ boolean groupEditing = false;
+
+ // ////////////////////////////////////////
+ // ///Everything below this is for defining the boundary of the rubberband
+ // ////////////////////////////////////////
+ int oldSeq = -1;
+
+ boolean changeEndSeq = false;
+
+ boolean changeStartSeq = false;
+
+ boolean changeEndRes = false;
+
+ boolean changeStartRes = false;
+
+ SequenceGroup stretchGroup = null;
+
+ boolean remove = false;
+
+ Point lastMousePress;
+
+ boolean mouseWheelPressed = false;
+
+ StringBuffer keyboardNo1;
+
+ StringBuffer keyboardNo2;
+
+ java.net.URL linkImageURL;
+
+ private final SequenceAnnotationReport seqARep;
+
+ StringBuilder tooltipText = new StringBuilder();
+
+ String tmpString;
+
+ EditCommand editCommand;
+
+ StructureSelectionManager ssm;
+
+ SearchResultsI lastSearchResults;
+
+ /**
+ * Creates a new SeqPanel object.
+ *
+ * @param avp
+ * DOCUMENT ME!
+ * @param p
+ * DOCUMENT ME!
+ */
+ public SeqPanel(AlignViewport av, AlignmentPanel ap)
+ {
+ linkImageURL = getClass().getResource("/images/link.gif");
+ seqARep = new SequenceAnnotationReport(linkImageURL.toString());
+ ToolTipManager.sharedInstance().registerComponent(this);
+ ToolTipManager.sharedInstance().setInitialDelay(0);
+ ToolTipManager.sharedInstance().setDismissDelay(10000);
+ this.av = av;
+ setBackground(Color.white);
+
+ seqCanvas = new SeqCanvas(ap);
+ setLayout(new BorderLayout());
+ add(seqCanvas, BorderLayout.CENTER);
+
+ this.ap = ap;
+
+ if (!av.isDataset())
+ {
+ addMouseMotionListener(this);
+ addMouseListener(this);
+ addMouseWheelListener(this);
+ ssm = av.getStructureSelectionManager();
+ ssm.addStructureViewerListener(this);
+ ssm.addSelectionListener(this);
+ }
+
+ lastMouseColumn = -1;
+ lastMouseSeq = -1;
+ }
+
+ int startWrapBlock = -1;
+
+ int wrappedBlock = -1;
+
+ /**
+ * Returns the aligned sequence position (base 0) at the mouse position, or
+ * the closest visible one
+ *
+ * @param evt
+ * @return
+ */
+ int findColumn(MouseEvent evt)
+ {
+ int res = 0;
+ int x = evt.getX();
+
+ int startRes = av.getRanges().getStartRes();
+ if (av.getWrapAlignment())
+ {
+
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += av.getCharHeight();
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap + seqCanvas.getAnnotationHeight();
+
+ int y = evt.getY();
+ y = Math.max(0, y - hgap);
+ x = Math.max(0, x - seqCanvas.getLabelWidthWest());
+
+ int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
+ if (cwidth < 1)
+ {
+ return 0;
+ }
+
+ wrappedBlock = y / cHeight;
+ wrappedBlock += startRes / cwidth;
+ // allow for wrapped view scrolled right (possible from Overview)
+ int startOffset = startRes % cwidth;
+ res = wrappedBlock * cwidth + startOffset
+ + +Math.min(cwidth - 1, x / av.getCharWidth());
+ }
+ else
+ {
+ if (x > seqCanvas.getX() + seqCanvas.getWidth())
+ {
+ // make sure we calculate relative to visible alignment, rather than
+ // right-hand gutter
+ x = seqCanvas.getX() + seqCanvas.getWidth();
+ }
+ res = (x / av.getCharWidth()) + startRes;
+ if (res > av.getRanges().getEndRes())
+ {
+ // moused off right
+ res = av.getRanges().getEndRes();
+ }
+ }
+
+ if (av.hasHiddenColumns())
+ {
+ res = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(res);
+ }
+
+ return res;
+
+ }
+
+ int findSeq(MouseEvent evt)
+ {
+ int seq = 0;
+ int y = evt.getY();
+
+ if (av.getWrapAlignment())
+ {
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
+ {
+ hgap += av.getCharHeight();
+ }
+
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight()
+ + hgap + seqCanvas.getAnnotationHeight();
+
+ y -= hgap;
+
+ seq = Math.min((y % cHeight) / av.getCharHeight(),
+ av.getAlignment().getHeight() - 1);
+ }
+ else
+ {
+ seq = Math.min(
+ (y / av.getCharHeight()) + av.getRanges().getStartSeq(),
+ av.getAlignment().getHeight() - 1);
+ }
+
+ return seq;
+ }
+
+ /**
+ * When all of a sequence of edits are complete, put the resulting edit list
+ * on the history stack (undo list), and reset flags for editing in progress.
+ */
+ void endEditing()
+ {
+ try
+ {
+ if (editCommand != null && editCommand.getSize() > 0)
+ {
+ ap.alignFrame.addHistoryItem(editCommand);
+ av.firePropertyChange("alignment", null,
+ av.getAlignment().getSequences());
+ }
+ } finally
+ {
+ /*
+ * Tidy up come what may...
+ */
+ 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 = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+ seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1;
+ scrollToVisible();
+ }
+
+ void moveCursor(int dx, int dy)
+ {
+ seqCanvas.cursorX += dx;
+ seqCanvas.cursorY += dy;
+
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+
+ if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
+ {
+ int original = seqCanvas.cursorX - dx;
+ int maxWidth = av.getAlignment().getWidth();
+
+ while (!hidden.isVisible(seqCanvas.cursorX)
+ && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0)
+ {
+ seqCanvas.cursorX += dx;
+ }
+
+ if (seqCanvas.cursorX >= maxWidth
+ || !hidden.isVisible(seqCanvas.cursorX))
+ {
+ seqCanvas.cursorX = original;
+ }
+ }
+
+ scrollToVisible();
+ }
+
+ void scrollToVisible()
+ {
+ if (seqCanvas.cursorX < 0)
+ {
+ seqCanvas.cursorX = 0;
+ }
+ else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1)
+ {
+ seqCanvas.cursorX = av.getAlignment().getWidth() - 1;
+ }
+
+ if (seqCanvas.cursorY < 0)
+ {
+ seqCanvas.cursorY = 0;
+ }
+ else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1)
+ {
+ seqCanvas.cursorY = av.getAlignment().getHeight() - 1;
+ }
+
+ endEditing();
+ if (av.getWrapAlignment())
+ {
+ av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX);
+ }
+ else
+ {
+ av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
+ }
+ setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
+ seqCanvas.cursorX, seqCanvas.cursorY);
+
+ seqCanvas.repaint();
+ }
+
+ void setSelectionAreaAtCursor(boolean topLeft)
+ {
+ SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
+
+ if (av.getSelectionGroup() != null)
+ {
+ SequenceGroup sg = av.getSelectionGroup();
+ // Find the top and bottom of this group
+ int min = av.getAlignment().getHeight(), max = 0;
+ for (int i = 0; i < sg.getSize(); i++)
+ {
+ int index = av.getAlignment().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).clear();
+ for (int i = min; i < max; i++)
+ {
+ sg.addSequence(av.getAlignment().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, false);
+ av.sendSelection();
+ }
+
+ void insertGapAtCursor(boolean group)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1());
+ endEditing();
+ }
+
+ void deleteGapAtCursor(boolean group)
+ {
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX + getKeyboardNo1();
+ editSequence(false, false, seqCanvas.cursorX);
+ endEditing();
+ }
+
+ void insertNucAtCursor(boolean group, String nuc)
+ {
+ // TODO not called - delete?
+ groupEditing = group;
+ startseq = seqCanvas.cursorY;
+ lastres = seqCanvas.cursorX;
+ editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1());
+ endEditing();
+ }
+
+ void numberPressed(char value)
+ {
+ if (keyboardNo1 == null)
+ {
+ keyboardNo1 = new StringBuffer();
+ }
+
+ if (keyboardNo2 != null)
+ {
+ keyboardNo2.append(value);
+ }
+ else
+ {
+ keyboardNo1.append(value);
+ }
+ }
+
+ int getKeyboardNo1()
+ {
+ try
+ {
+ if (keyboardNo1 != null)
+ {
+ int value = Integer.parseInt(keyboardNo1.toString());
+ keyboardNo1 = null;
+ return value;
+ }
+ } catch (Exception x)
+ {
+ }
+ keyboardNo1 = null;
+ return 1;
+ }
+
+ int getKeyboardNo2()
+ {
+ try
+ {
+ if (keyboardNo2 != null)
+ {
+ int value = Integer.parseInt(keyboardNo2.toString());
+ keyboardNo2 = null;
+ return value;
+ }
+ } catch (Exception x)
+ {
+ }
+ keyboardNo2 = null;
+ return 1;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ boolean didDrag = mouseDragging; // did we come here after a drag
+ mouseDragging = false;
+ mouseWheelPressed = false;
+
+ if (evt.isPopupTrigger()) // Windows: mouseReleased
+ {
+ showPopupMenu(evt);
+ evt.consume();
+ return;
+ }
+
+ if (!editingSeqs)
+ {
+ doMouseReleasedDefineMode(evt, didDrag);
+ return;
+ }
+
+ endEditing();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ lastMousePress = evt.getPoint();
+
+ if (SwingUtilities.isMiddleMouseButton(evt))
+ {
+ mouseWheelPressed = true;
+ return;
+ }
+
+ boolean isControlDown = Platform.isControlDown(evt);
+ if (evt.isShiftDown() || isControlDown)
+ {
+ editingSeqs = true;
+ if (isControlDown)
+ {
+ groupEditing = true;
+ }
+ }
+ else
+ {
+ doMousePressedDefineMode(evt);
+ return;
+ }
+
+ int seq = findSeq(evt);
+ int res = findColumn(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;
+ }
+
+ String lastMessage;
+
+ @Override
+ public void mouseOverSequence(SequenceI sequence, int index, int pos)
+ {
+ String tmp = sequence.hashCode() + " " + index + " " + pos;
+
+ if (lastMessage == null || !lastMessage.equals(tmp))
+ {
+ // System.err.println("mouseOver Sequence: "+tmp);
+ ssm.mouseOverSequence(sequence, index, pos, av);
+ }
+ lastMessage = tmp;
+ }
+
+ /**
+ * Highlight the mapped region described by the search results object (unless
+ * unchanged). This supports highlight of protein while mousing over linked
+ * cDNA and vice versa. The status bar is also updated to show the location of
+ * the start of the highlighted region.
+ */
+ @Override
+ public void highlightSequence(SearchResultsI results)
+ {
+ if (results == null || results.equals(lastSearchResults))
+ {
+ return;
+ }
+ lastSearchResults = results;
+
+ boolean wasScrolled = false;
+
+ if (av.isFollowHighlight())
+ {
+ // don't allow highlight of protein/cDNA to also scroll a complementary
+ // panel,as this sets up a feedback loop (scrolling panel 1 causes moused
+ // over residue to change abruptly, causing highlighted residue in panel 2
+ // to change, causing a scroll in panel 1 etc)
+ ap.setToScrollComplementPanel(false);
+ wasScrolled = ap.scrollToPosition(results, false);
+ if (wasScrolled)
+ {
+ seqCanvas.revalidate();
+ }
+ ap.setToScrollComplementPanel(true);
+ }
+
+ boolean noFastPaint = wasScrolled && av.getWrapAlignment();
+ if (seqCanvas.highlightSearchResults(results, noFastPaint))
+ {
+ setStatusMessage(results);
+ }
+ }
+
+ @Override
+ public VamsasSource getVamsasSource()
+ {
+ return this.ap == null ? null : this.ap.av;
+ }
+
+ @Override
+ public void updateColours(SequenceI seq, int index)
+ {
+ System.out.println("update the seqPanel colours");
+ // repaint();
+ }
+
+ /**
+ * Action on mouse movement is to update the status bar to show the current
+ * sequence position, and (if features are shown) to show any features at the
+ * position in a tooltip. Does nothing if the mouse move does not change
+ * residue position.
+ *
+ * @param evt
+ */
+ @Override
+ public void mouseMoved(MouseEvent evt)
+ {
+ if (editingSeqs)
+ {
+ // This is because MacOSX creates a mouseMoved
+ // If control is down, other platforms will not.
+ mouseDragged(evt);
+ }
+
+ final int column = findColumn(evt);
+ final int seq = findSeq(evt);
+
+ if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+ {
+ lastMouseSeq = -1;
+ return;
+ }
+ if (column == lastMouseColumn && seq == lastMouseSeq)
+ {
+ /*
+ * just a pixel move without change of residue
+ */
+ return;
+ }
+ lastMouseColumn = column;
+ lastMouseSeq = seq;
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+ if (column >= sequence.getLength())
+ {
+ return;
+ }
+
+ /*
+ * set status bar message, returning residue position in sequence
+ */
+ boolean isGapped = Comparison.isGap(sequence.getCharAt(column));
+ final int pos = setStatusMessage(sequence, column, seq);
+ if (ssm != null && !isGapped)
+ {
+ mouseOverSequence(sequence, column, pos);
+ }
+
+ tooltipText.setLength(6); // Cuts the buffer back to <html>
+
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
+ if (groups != null)
+ {
+ for (int g = 0; g < groups.length; g++)
+ {
+ if (groups[g].getStartRes() <= column
+ && groups[g].getEndRes() >= column)
+ {
+ 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());
+ }
+ }
+ }
+ }
+
+ /*
+ * add any features at the position to the tooltip; if over a gap, only
+ * add features that straddle the gap (pos may be the residue before or
+ * after the gap)
+ */
+ if (av.isShowSequenceFeatures())
+ {
+ List<SequenceFeature> features = ap.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+ seqARep.appendFeatures(tooltipText, pos, features,
+ this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
+ }
+ if (tooltipText.length() == 6) // <html>
+ {
+ setToolTipText(null);
+ lastTooltip = null;
+ }
+ else
+ {
+ String textString = tooltipText.toString();
+ if (lastTooltip == null || !lastTooltip.equals(textString))
+ {
+ String formattedTooltipText = JvSwingUtils.wrapTooltip(true,
+ textString);
+ setToolTipText(formattedTooltipText);
+ lastTooltip = textString;
+ }
+ }
+ }
+
+ private Point lastp = null;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent)
+ */
+ @Override
+ public Point getToolTipLocation(MouseEvent event)
+ {
+ int x = event.getX(), w = getWidth();
+ int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too
+ // close to edge
+ Point p = lastp;
+ if (!event.isShiftDown() || p == null)
+ {
+ p = (tooltipText != null && tooltipText.length() > 6)
+ ? new Point(event.getX() + wdth, event.getY() - 20)
+ : null;
+ }
+ /*
+ * TODO: try to modify position region is not obcured by tooltip
+ */
+ return lastp = p;
+ }
+
+ String lastTooltip;
+
+ /**
+ * set when the current UI interaction has resulted in a change that requires
+ * shading in overviews and structures to be recalculated. this could be
+ * changed to a something more expressive that indicates what actually has
+ * changed, so selective redraws can be applied (ie. only structures, only
+ * overview, etc)
+ */
+ private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller
+
+ /**
+ * set if av.getSelectionGroup() refers to a group that is defined on the
+ * alignment view, rather than a transient selection
+ */
+ // private boolean editingDefinedGroup = false; // TODO: refactor to
+ // avcontroller or viewModel
+
+ /**
+ * Sets the status message in alignment panel, showing the sequence number
+ * (index) and id, and residue and residue position if not at a gap, for the
+ * given sequence and column position. Returns the residue position returned
+ * by Sequence.findPosition. Note this may be for the nearest adjacent residue
+ * if at a gapped position.
+ *
+ * @param sequence
+ * aligned sequence object
+ * @param column
+ * alignment column
+ * @param seqIndex
+ * index of sequence in alignment
+ * @return sequence position of residue at column, or adjacent residue if at a
+ * gap
+ */
+ int setStatusMessage(SequenceI sequence, final int column, int seqIndex)
+ {
+ char sequenceChar = sequence.getCharAt(column);
+ int pos = sequence.findPosition(column);
+ setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+
+ return pos;
+ }
+
+ /**
+ * Builds the status message for the current cursor location and writes it to
+ * the status bar, for example
+ *
+ * <pre>
+ * Sequence 3 ID: FER1_SOLLC
+ * Sequence 5 ID: FER1_PEA Residue: THR (4)
+ * Sequence 5 ID: FER1_PEA Residue: B (3)
+ * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+ * </pre>
+ *
+ * @param sequence
+ * @param seqIndex
+ * sequence position in the alignment (1..)
+ * @param sequenceChar
+ * the character under the cursor
+ * @param residuePos
+ * the sequence residue position (if not over a gap)
+ */
+ protected void setStatusMessage(SequenceI sequence, int seqIndex,
+ char sequenceChar, int residuePos)
+ {
+ StringBuilder text = new StringBuilder(32);
+
+ /*
+ * Sequence number (if known), and sequence name.
+ */
+ String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
+ text.append("Sequence").append(seqno).append(" ID: ")
+ .append(sequence.getName());
+
+ String residue = null;
+
+ /*
+ * Try to translate the display character to residue name (null for gap).
+ */
+ boolean isGapped = Comparison.isGap(sequenceChar);
+
+ if (!isGapped)
+ {
+ boolean nucleotide = av.getAlignment().isNucleotide();
+ String displayChar = String.valueOf(sequenceChar);
+ if (nucleotide)
+ {
+ residue = ResidueProperties.nucleotideName.get(displayChar);
+ }
+ else
+ {
+ residue = "X".equalsIgnoreCase(displayChar) ? "X"
+ : ("*".equals(displayChar) ? "STOP"
+ : ResidueProperties.aa2Triplet.get(displayChar));
+ }
+ text.append(" ").append(nucleotide ? "Nucleotide" : "Residue")
+ .append(": ").append(residue == null ? displayChar : residue);
+
+ text.append(" (").append(Integer.toString(residuePos)).append(")");
+ }
+ ap.alignFrame.statusBar.setText(text.toString());
+ }
+
+ /**
+ * Set the status bar message to highlight the first matched position in
+ * search results.
+ *
+ * @param results
+ */
+ private void setStatusMessage(SearchResultsI results)
+ {
+ AlignmentI al = this.av.getAlignment();
+ int sequenceIndex = al.findIndex(results);
+ if (sequenceIndex == -1)
+ {
+ return;
+ }
+ SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+ for (SearchResultMatchI m : results.getResults())
+ {
+ SequenceI seq = m.getSequence();
+ if (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+
+ if (seq == ds)
+ {
+ int start = m.getStart();
+ setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
+ start);
+ return;
+ }
+ }
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (mouseWheelPressed)
+ {
+ boolean inSplitFrame = ap.av.getCodingComplement() != null;
+ boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna();
+
+ int oldWidth = av.getCharWidth();
+
+ // Which is bigger, left-right or up-down?
+ if (Math.abs(evt.getY() - lastMousePress.getY()) > Math
+ .abs(evt.getX() - lastMousePress.getX()))
+ {
+ /*
+ * on drag up or down, decrement or increment font size
+ */
+ int fontSize = av.font.getSize();
+ boolean fontChanged = false;
+
+ if (evt.getY() < lastMousePress.getY())
+ {
+ fontChanged = true;
+ fontSize--;
+ }
+ else if (evt.getY() > lastMousePress.getY())
+ {
+ fontChanged = true;
+ fontSize++;
+ }
+
+ if (fontSize < 1)
+ {
+ fontSize = 1;
+ }
+
+ if (fontChanged)
+ {
+ Font newFont = new Font(av.font.getName(), av.font.getStyle(),
+ fontSize);
+ av.setFont(newFont, true);
+ av.setCharWidth(oldWidth);
+ ap.fontChanged();
+ if (copyChanges)
+ {
+ ap.av.getCodingComplement().setFont(newFont, true);
+ SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+ .getSplitViewContainer();
+ splitFrame.adjustLayout();
+ splitFrame.repaint();
+ }
+ }
+ }
+ else
+ {
+ /*
+ * on drag left or right, decrement or increment character width
+ */
+ int newWidth = 0;
+ if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1)
+ {
+ newWidth = av.getCharWidth() - 1;
+ av.setCharWidth(newWidth);
+ }
+ else if (evt.getX() > lastMousePress.getX())
+ {
+ newWidth = av.getCharWidth() + 1;
+ av.setCharWidth(newWidth);
+ }
+ if (newWidth > 0)
+ {
+ ap.paintAlignment(false, false);
+ if (copyChanges)
+ {
+ /*
+ * need to ensure newWidth is set on cdna, regardless of which
+ * panel the mouse drag happened in; protein will compute its
+ * character width as 1:1 or 3:1
+ */
+ av.getCodingComplement().setCharWidth(newWidth);
+ SplitFrame splitFrame = (SplitFrame) ap.alignFrame
+ .getSplitViewContainer();
+ splitFrame.adjustLayout();
+ splitFrame.repaint();
+ }
+ }
+ }
+
+ FontMetrics fm = getFontMetrics(av.getFont());
+ av.validCharWidth = fm.charWidth('M') <= av.getCharWidth();
+
+ lastMousePress = evt.getPoint();
+
+ return;
+ }
+
+ if (!editingSeqs)
+ {
+ doMouseDraggedDefineMode(evt);
+ return;
+ }
+
+ int res = findColumn(evt);
+
+ if (res < 0)
+ {
+ res = 0;
+ }
+
+ if ((lastres == -1) || (lastres == res))
+ {
+ return;
+ }
+
+ if ((res < av.getAlignment().getWidth()) && (res < lastres))
+ {
+ // dragLeft, delete gap
+ editSequence(false, false, res);
+ }
+ else
+ {
+ editSequence(true, false, res);
+ }
+
+ mouseDragging = true;
+ if ((scrollThread != null) && (scrollThread.isRunning()))
+ {
+ scrollThread.setEvent(evt);
+ }
+ }
+
+ // TODO: Make it more clever than many booleans
+ synchronized void editSequence(boolean insertGap, boolean editSeq,
+ int startres)
+ {
+ int fixedLeft = -1;
+ int fixedRight = -1;
+ boolean fixedColumns = false;
+ SequenceGroup sg = av.getSelectionGroup();
+
+ SequenceI seq = av.getAlignment().getSequenceAt(startseq);
+
+ // No group, but the sequence may represent a group
+ if (!groupEditing && av.hasHiddenRows())
+ {
+ if (av.isHiddenRepSequence(seq))
+ {
+ sg = av.getRepresentedSequences(seq);
+ groupEditing = true;
+ }
+ }
+
+ StringBuilder message = new StringBuilder(64);
+ if (groupEditing)
+ {
+ message.append("Edit group:");
+ if (editCommand == null)
+ {
+ editCommand = new EditCommand(
+ MessageManager.getString("action.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(MessageManager
+ .formatMessage("label.edit_params", new String[]
+ { 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.getHiddenRepSequences()).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.isHiddenRepSequence(seq))
+ {
+ endEditing();
+ return;
+ }
+ sg = av.getRepresentedSequences(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.getAlignment().getHiddenColumns()
+ .getHiddenBoundaryLeft(startres);
+ int y2 = av.getAlignment().getHiddenColumns()
+ .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)
+ {
+ List<SequenceI> vseqs = sg.getSequences(av.getHiddenRepSequences());
+ int g, groupSize = vseqs.size();
+ SequenceI[] groupSeqs = new SequenceI[groupSize];
+ for (g = 0; g < groupSeqs.length; g++)
+ {
+ groupSeqs[g] = vseqs.get(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.getAlignment().getWidth() - 1)
+ {
+ sg.setEndRes(av.getAlignment().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 > lastres; fixedRight--)
+ {
+ blank = true;
+
+ for (g = 0; g < groupSize; g++)
+ {
+ for (int j = 0; j < startres - lastres; j++)
+ {
+ if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j)))
+ {
+ blank = false;
+ break;
+ }
+ }
+ }
+ if (blank)
+ {
+ break;
+ }
+ }
+
+ if (!blank)
+ {
+ if (sg.getSize() == av.getAlignment().getHeight())
+ {
+ if ((av.hasHiddenColumns() && startres < av.getAlignment()
+ .getHiddenColumns().getHiddenBoundaryRight(startres)))
+ {
+ endEditing();
+ return;
+ }
+
+ int alWidth = av.getAlignment().getWidth();
+ if (av.hasHiddenRows())
+ {
+ int hwidth = av.getAlignment().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 (!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
+ {
+ appendEdit(Action.INSERT_GAP, groupSeqs, startres,
+ startres - lastres);
+ }
+ }
+ else
+ {
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j > startres; j--)
+ {
+ deleteChar(startres, groupSeqs, fixedRight);
+ }
+ }
+ else
+ {
+ appendEdit(Action.DELETE_GAP, groupSeqs, startres,
+ lastres - startres);
+ }
+
+ }
+ }
+ 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
+ {
+ appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres,
+ startres - lastres);
+ }
+ }
+ else
+ {
+ if (!editSeq)
+ {
+ // dragging to the left
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j > startres; j--)
+ {
+ if (!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 (!Comparison.isGap(seq.getCharAt(m)))
+ {
+ break;
+ }
+ max++;
+ }
+
+ if (max > 0)
+ {
+ appendEdit(Action.DELETE_GAP, new SequenceI[] { seq },
+ startres, max);
+ }
+ }
+ }
+ else
+ {// insertGap==false AND editSeq==TRUE;
+ if (fixedColumns && fixedRight != -1)
+ {
+ for (int j = lastres; j < startres; j++)
+ {
+ insertChar(j, new SequenceI[] { seq }, fixedRight);
+ }
+ }
+ else
+ {
+ appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres,
+ startres - lastres);
+ }
+ }
+ }
+ }
+
+ 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 (Comparison.isGap(seq[s].getCharAt(blankColumn)))
+ {
+ // Theres a space, so break and insert the gap
+ break;
+ }
+ }
+
+ if (blankColumn <= j)
+ {
+ blankColumn = fixedColumn;
+ endEditing();
+ return;
+ }
+ }
+
+ appendEdit(Action.DELETE_GAP, seq, blankColumn, 1);
+
+ appendEdit(Action.INSERT_GAP, seq, j, 1);
+
+ }
+
+ /**
+ * Helper method to add and perform one edit action.
+ *
+ * @param action
+ * @param seq
+ * @param pos
+ * @param count
+ */
+ protected void appendEdit(Action action, SequenceI[] seq, int pos,
+ int count)
+ {
+
+ final Edit edit = new EditCommand().new Edit(action, seq, pos, count,
+ av.getAlignment().getGapCharacter());
+
+ editCommand.appendEdit(edit, av.getAlignment(), true, null);
+ }
+
+ void deleteChar(int j, SequenceI[] seq, int fixedColumn)
+ {
+
+ appendEdit(Action.DELETE_GAP, seq, j, 1);
+
+ appendEdit(Action.INSERT_GAP, seq, fixedColumn, 1);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ if (oldSeq < 0)
+ {
+ oldSeq = 0;
+ }
+
+ if ((scrollThread != null) && (scrollThread.isRunning()))
+ {
+ scrollThread.stopScrolling();
+ scrollThread = null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseExited(MouseEvent e)
+ {
+ if (av.getWrapAlignment())
+ {
+ return;
+ }
+
+ if (mouseDragging && scrollThread == null)
+ {
+ scrollThread = new ScrollThread();
+ }
+ }
+
+ /**
+ * Handler for double-click on a position with one or more sequence features.
+ * Opens the Amend Features dialog to allow feature details to be amended, or
+ * the feature deleted.
+ */
+ @Override
+ public void mouseClicked(MouseEvent evt)
+ {
+ SequenceGroup sg = null;
+ SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt));
+ if (evt.getClickCount() > 1)
+ {
+ sg = av.getSelectionGroup();
+ if (sg != null && sg.getSize() == 1
+ && sg.getEndRes() - sg.getStartRes() < 2)
+ {
+ av.setSelectionGroup(null);
+ }
+
+ int column = findColumn(evt);
+
+ /*
+ * find features at the position (if not gapped), or straddling
+ * the position (if at a gap)
+ */
+ List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+
+ if (!features.isEmpty())
+ {
+ /*
+ * highlight the first feature at the position on the alignment
+ */
+ SearchResultsI highlight = new SearchResults();
+ highlight.addResult(sequence, features.get(0).getBegin(), features
+ .get(0).getEnd());
+ seqCanvas.highlightSearchResults(highlight, false);
+
+ /*
+ * open the Amend Features dialog; clear highlighting afterwards,
+ * whether changes were made or not
+ */
+ List<SequenceI> seqs = Collections.singletonList(sequence);
+ seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false,
+ ap);
+ av.setSearchResults(null); // clear highlighting
+ seqCanvas.repaint(); // draw new/amended features
+ }
+ }
+ }
+
+ @Override
+ public void mouseWheelMoved(MouseWheelEvent e)
+ {
+ e.consume();
+ if (e.getWheelRotation() > 0)
+ {
+ if (e.isShiftDown())
+ {
+ av.getRanges().scrollRight(true);
+
+ }
+ else
+ {
+ av.getRanges().scrollUp(false);
+ }
+ }
+ else
+ {
+ if (e.isShiftDown())
+ {
+ av.getRanges().scrollRight(false);
+ }
+ else
+ {
+ av.getRanges().scrollUp(true);
+ }
+ }
+
+ /*
+ * update status bar and tooltip for new position
+ * (need to synthesize a mouse movement to refresh tooltip)
+ */
+ mouseMoved(e);
+ ToolTipManager.sharedInstance().mouseMoved(e);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void doMousePressedDefineMode(MouseEvent evt)
+ {
+ final int res = findColumn(evt);
+ final int seq = findSeq(evt);
+ oldSeq = seq;
+ updateOverviewAndStructs = false;
+
+ startWrapBlock = wrappedBlock;
+
+ if (av.getWrapAlignment() && seq > av.getAlignment().getHeight())
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString(
+ "label.cannot_edit_annotations_in_wrapped_view"),
+ MessageManager.getString("label.wrapped_view_no_edit"),
+ JvOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ if (seq < 0 || res < 0)
+ {
+ return;
+ }
+
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+ if ((sequence == null) || (res > sequence.getLength()))
+ {
+ return;
+ }
+
+ stretchGroup = av.getSelectionGroup();
+
+ if (stretchGroup == null || !stretchGroup.contains(sequence, res))
+ {
+ stretchGroup = av.getAlignment().findGroup(sequence, res);
+ if (stretchGroup != null)
+ {
+ // only update the current selection if the popup menu has a group to
+ // focus on
+ av.setSelectionGroup(stretchGroup);
+ }
+ }
+
+ if (evt.isPopupTrigger()) // Mac: mousePressed
+ {
+ showPopupMenu(evt);
+ return;
+ }
+
+ /*
+ * defer right-mouse click handling to mouseReleased on Windows
+ * (where isPopupTrigger() will answer true)
+ * NB isRightMouseButton is also true for Cmd-click on Mac
+ */
+ if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac())
+ {
+ return;
+ }
+
+ if (av.cursorMode)
+ {
+ seqCanvas.cursorX = findColumn(evt);
+ seqCanvas.cursorY = findSeq(evt);
+ seqCanvas.repaint();
+ return;
+ }
+
+ if (stretchGroup == null)
+ {
+ createStretchGroup(res, sequence);
+ }
+
+ if (stretchGroup != null)
+ {
+ stretchGroup.addPropertyChangeListener(seqCanvas);
+ }
+
+ seqCanvas.repaint();
+ }
+
+ private void createStretchGroup(int res, SequenceI sequence)
+ {
+ // 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.getResidueShading(),
+ ap.getViewName());
+ }
+
+ if (av.getAbovePIDThreshold())
+ {
+ SliderPanel.setPIDSliderSource(ap, av.getResidueShading(),
+ ap.getViewName());
+ }
+ // TODO: stretchGroup will always be not null. Is this a merge error ?
+ // or is there a threading issue here?
+ 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();
+
+ }
+
+ /**
+ * Build and show a pop-up menu at the right-click mouse position
+ *
+ * @param evt
+ * @param res
+ * @param sequences
+ */
+ void showPopupMenu(MouseEvent evt)
+ {
+ final int column = findColumn(evt);
+ final int seq = findSeq(evt);
+ SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+ List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
+ .findFeaturesAtColumn(sequence, column + 1);
+ List<String> links = new ArrayList<>();
+ for (SequenceFeature sf : allFeatures)
+ {
+ if (sf.links != null)
+ {
+ for (String link : sf.links)
+ {
+ links.add(link);
+ }
+ }
+ }
+
+ PopupMenu pop = new PopupMenu(ap, null, links);
+ pop.show(this, evt.getX(), evt.getY());
+ }
+
+ /**
+ * Update the display after mouse up on a selection or group
+ *
+ * @param evt
+ * mouse released event details
+ * @param afterDrag
+ * true if this event is happening after a mouse drag (rather than a
+ * mouse down)
+ */
+ public void doMouseReleasedDefineMode(MouseEvent evt, boolean afterDrag)
+ {
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ stretchGroup.removePropertyChangeListener(seqCanvas);
+
+ // always do this - annotation has own state
+ // but defer colourscheme update until hidden sequences are passed in
+ boolean vischange = stretchGroup.recalcConservation(true);
+ updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup()
+ && afterDrag;
+ if (stretchGroup.cs != null)
+ {
+ stretchGroup.cs.alignmentChanged(stretchGroup,
+ av.getHiddenRepSequences());
+
+ ResidueShaderI groupColourScheme = stretchGroup
+ .getGroupColourScheme();
+ String name = stretchGroup.getName();
+ if (stretchGroup.cs.conservationApplied())
+ {
+ SliderPanel.setConservationSlider(ap, groupColourScheme, name);
+ }
+ if (stretchGroup.cs.getThreshold() > 0)
+ {
+ SliderPanel.setPIDSliderSource(ap, groupColourScheme, name);
+ }
+ }
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // TODO: structure colours only need updating if stretchGroup used to or now
+ // does contain sequences with structure views
+ ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs);
+ updateOverviewAndStructs = false;
+ changeEndRes = false;
+ changeStartRes = false;
+ stretchGroup = null;
+ av.sendSelection();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void doMouseDraggedDefineMode(MouseEvent evt)
+ {
+ int res = findColumn(evt);
+ int y = findSeq(evt);
+
+ if (wrappedBlock != startWrapBlock)
+ {
+ return;
+ }
+
+ if (stretchGroup == null)
+ {
+ return;
+ }
+
+ if (res >= av.getAlignment().getWidth())
+ {
+ res = av.getAlignment().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.getRanges().getStartRes())
+ {
+ res = av.getRanges().getStartRes();
+ }
+
+ if (changeEndRes)
+ {
+ if (res > (stretchGroup.getStartRes() - 1))
+ {
+ stretchGroup.setEndRes(res);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
+ }
+ }
+ else if (changeStartRes)
+ {
+ if (res < (stretchGroup.getEndRes() + 1))
+ {
+ stretchGroup.setStartRes(res);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
+ }
+ }
+
+ int dragDirection = 0;
+
+ if (y > oldSeq)
+ {
+ dragDirection = 1;
+ }
+ else if (y < oldSeq)
+ {
+ dragDirection = -1;
+ }
+
+ while ((y != oldSeq) && (oldSeq > -1)
+ && (y < av.getAlignment().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);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
+ }
+ else
+ {
+ if (seq != null)
+ {
+ stretchGroup.addSequence(seq, false);
+ }
+
+ stretchGroup.addSequence(nextSeq, false);
+ updateOverviewAndStructs |= av.isSelectionDefinedGroup();
+ }
+ }
+
+ if (oldSeq < 0)
+ {
+ oldSeq = -1;
+ }
+
+ mouseDragging = true;
+
+ if ((scrollThread != null) && (scrollThread.isRunning()))
+ {
+ scrollThread.setEvent(evt);
+ }
+ }
+
+ void scrollCanvas(MouseEvent evt)
+ {
+ if (evt == null)
+ {
+ if ((scrollThread != null) && (scrollThread.isRunning()))
+ {
+ scrollThread.stopScrolling();
+ 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;
+
+ private volatile boolean threadRunning = true;
+
+ public ScrollThread()
+ {
+ start();
+ }
+
+ public void setEvent(MouseEvent e)
+ {
+ evt = e;
+ }
+
+ public void stopScrolling()
+ {
+ threadRunning = false;
+ }
+
+ public boolean isRunning()
+ {
+ return threadRunning;
+ }
+
+ @Override
+ public void run()
+ {
+ while (threadRunning)
+ {
+ if (evt != null)
+ {
+ if (mouseDragging && (evt.getY() < 0)
+ && (av.getRanges().getStartSeq() > 0))
+ {
+ av.getRanges().scrollUp(true);
+ }
+
+ if (mouseDragging && (evt.getY() >= getHeight()) && (av
+ .getAlignment().getHeight() > av.getRanges().getEndSeq()))
+ {
+ av.getRanges().scrollUp(false);
+ }
+
+ if (mouseDragging && (evt.getX() < 0))
+ {
+ av.getRanges().scrollRight(false);
+ }
+ else if (mouseDragging && (evt.getX() >= getWidth()))
+ {
+ av.getRanges().scrollRight(true);
+ }
+ }
+
+ try
+ {
+ Thread.sleep(20);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ }
+
+ /**
+ * modify current selection according to a received message.
+ */
+ @Override
+ public void selection(SequenceGroup seqsel, ColumnSelection colsel,
+ HiddenColumns hidden, 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.
+ boolean iSentTheSelection = (av == source
+ || (source instanceof AlignViewport
+ && ((AlignmentViewport) source).getSequenceSetId()
+ .equals(av.getSequenceSetId())));
+
+ if (iSentTheSelection)
+ {
+ // respond to our own event by updating dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ return;
+ }
+
+ // process further ?
+ if (!av.followSelection)
+ {
+ return;
+ }
+
+ /*
+ * Ignore the selection if there is one of our own pending.
+ */
+ if (av.isSelectionGroupChanged(false) || av.isColSelChanged(false))
+ {
+ return;
+ }
+
+ /*
+ * Check for selection in a view of which this one is a dna/protein
+ * complement.
+ */
+ if (selectionFromTranslation(seqsel, colsel, hidden, source))
+ {
+ return;
+ }
+
+ // do we want to thread this ? (contention with seqsel and colsel locks, I
+ // suspect)
+ /*
+ * only copy colsel if there is a real intersection between
+ * sequence selection and this panel's alignment
+ */
+ boolean repaint = false;
+ boolean copycolsel = false;
+
+ SequenceGroup sgroup = null;
+ if (seqsel != null && seqsel.getSize() > 0)
+ {
+ if (av.getAlignment() == null)
+ {
+ Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId()
+ + " ViewId=" + av.getViewId()
+ + " 's alignment is NULL! returning immediately.");
+ return;
+ }
+ sgroup = seqsel.intersect(av.getAlignment(),
+ (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null);
+ if ((sgroup != null && sgroup.getSize() > 0))
+ {
+ copycolsel = true;
+ }
+ }
+ if (sgroup != null && sgroup.getSize() > 0)
+ {
+ av.setSelectionGroup(sgroup);
+ }
+ else
+ {
+ av.setSelectionGroup(null);
+ }
+ av.isSelectionGroupChanged(true);
+ repaint = true;
+
+ if (copycolsel)
+ {
+ // the current selection is unset or from a previous message
+ // so import the new colsel.
+ if (colsel == null || colsel.isEmpty())
+ {
+ if (av.getColumnSelection() != null)
+ {
+ av.getColumnSelection().clear();
+ repaint = true;
+ }
+ }
+ else
+ {
+ // TODO: shift colSel according to the intersecting sequences
+ if (av.getColumnSelection() == null)
+ {
+ av.setColumnSelection(new ColumnSelection(colsel));
+ }
+ else
+ {
+ av.getColumnSelection().setElementsFrom(colsel,
+ av.getAlignment().getHiddenColumns());
+ }
+ }
+ av.isColSelChanged(true);
+ repaint = true;
+ }
+
+ if (copycolsel && av.hasHiddenColumns()
+ && (av.getAlignment().getHiddenColumns() == null))
+ {
+ System.err.println("Bad things");
+ }
+ if (repaint) // always true!
+ {
+ // probably finessing with multiple redraws here
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+ // ap.paintAlignment(false);
+ }
+
+ // lastly, update dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ }
+
+ /**
+ * If this panel is a cdna/protein translation view of the selection source,
+ * tries to map the source selection to a local one, and returns true. Else
+ * returns false.
+ *
+ * @param seqsel
+ * @param colsel
+ * @param source
+ */
+ protected boolean selectionFromTranslation(SequenceGroup seqsel,
+ ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
+ {
+ if (!(source instanceof AlignViewportI))
+ {
+ return false;
+ }
+ final AlignViewportI sourceAv = (AlignViewportI) source;
+ if (sourceAv.getCodingComplement() != av
+ && av.getCodingComplement() != sourceAv)
+ {
+ return false;
+ }
+
+ /*
+ * Map sequence selection
+ */
+ SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
+ av.setSelectionGroup(sg);
+ av.isSelectionGroupChanged(true);
+
+ /*
+ * Map column selection
+ */
+ // ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv,
+ // av);
+ ColumnSelection cs = new ColumnSelection();
+ HiddenColumns hs = new HiddenColumns();
+ MappingUtils.mapColumnSelection(colsel, hidden, sourceAv, av, cs, hs);
+ av.setColumnSelection(cs);
+ av.getAlignment().setHiddenColumns(hs);
+
+ // lastly, update any dependent dialogs
+ if (ap.getCalculationDialog() != null)
+ {
+ ap.getCalculationDialog().validateCalcTypes();
+ }
+
+ PaintRefresher.Refresh(this, av.getSequenceSetId());
+
+ return true;
+ }
+}