X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=162f978ab4adec11a87e246a6f35f6a8a2df3687;hb=e542a2b9968ee6a7def19e79e84c27684ee686e3;hp=36805030d98f3e5fb9d2cef849c9b6405f1b6519;hpb=f3030a08d2a57edf262374d822502c5aaafc0406;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 3680503..162f978 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -4,15 +4,14 @@ import java.awt.*; import java.awt.event.*; import jalview.datamodel.*; import javax.swing.*; +import java.util.*; import jalview.schemes.*; -import jalview.analysis.*; - public class SeqPanel extends JPanel { public SeqCanvas seqCanvas; - public AlignmentPanel parent; + public AlignmentPanel ap; protected int startres; protected int lastres; @@ -21,12 +20,15 @@ public class SeqPanel extends JPanel protected int startseq; protected int padseq; - public boolean editFlag; protected AlignViewport av; // if character is inserted or deleted, we will need to recalculate the conservation int seqEditOccurred = -1; + ScrollThread scrollThread = null; + boolean mouseDragging = false; + + public SeqPanel(AlignViewport avp, AlignmentPanel p) { this.av = avp; @@ -34,18 +36,24 @@ public class SeqPanel extends JPanel setLayout(new BorderLayout()); add(seqCanvas, BorderLayout.CENTER); - parent = p; + ap = p; addMouseMotionListener( new MouseMotionAdapter() { public void mouseMoved(MouseEvent evt) - { doMouseMoved(evt); } + { + if(av.getWrapAlignment()) + return; + doMouseMoved(evt); } + public void mouseDragged(MouseEvent evt) { - if(av.groupDefiningMode) - doMouseDraggedDefineMode(evt); - else + if(av.getWrapAlignment()) + return; + if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) doMouseDragged(evt); + else + doMouseDraggedDefineMode(evt); } }); @@ -53,17 +61,36 @@ public class SeqPanel extends JPanel { public void mouseReleased(MouseEvent evt) { - if(av.groupDefiningMode) - doMouseReleasedDefineMode(evt); - else + if(av.getWrapAlignment()) + return; + if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) doMouseReleased(evt); + else + doMouseReleasedDefineMode(evt); } public void mousePressed(MouseEvent evt) { - if(av.groupDefiningMode) - doMousePressedDefineMode(evt); - else + if(av.getWrapAlignment()) + return; + if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) doMousePressed(evt); + else + doMousePressedDefineMode(evt); + } + public void mouseExited(MouseEvent evt) + { + if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() || + evt.isControlDown()) + return; + doMouseExitedDefineMode(evt); + + } + public void mouseEntered(MouseEvent evt) + { + if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() || + evt.isControlDown()) + return; + doMouseEnteredDefineMode(evt); } }); @@ -78,8 +105,6 @@ public class SeqPanel extends JPanel endres = res; - // This is to detect edits - we're at the end of an edit if mouse is up - editFlag = false; startseq = -1; startres = -1; lastres = -1; @@ -88,13 +113,12 @@ public class SeqPanel extends JPanel seqEditOccurred = -1; - parent.RefreshPanels(); - repaint(); + ap.repaint(); } public void doMousePressed(MouseEvent evt) { - parent.alignFrame.addHistoryItem("sequence edit"); + ap.alignFrame.addHistoryItem("sequence edit"); int seq; int res; @@ -104,7 +128,8 @@ public class SeqPanel extends JPanel res = x/av.getCharWidth() + av.getStartRes(); seq = y/av.getCharHeight() + av.getStartSeq(); - if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength()) + 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 @@ -112,16 +137,17 @@ public class SeqPanel extends JPanel startseq = seq; - if (startseq == (av.getAlignment().getHeight()-1)) { + if (startseq == (av.getAlignment().getHeight() - 1)) padseq = 1; - } else { + else padseq = 1; - } startres = res; lastres = res; - } else { + } + else + { startseq = -1; startres = -1; lastres = -1; @@ -143,12 +169,9 @@ public class SeqPanel extends JPanel res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes(); - System.out.println( ((y/chunkHeight)*(getWidth()/av.charWidth)) +" "+((x / av.getCharWidth()) + av.getStartRes()) ); y %= chunkHeight; seq = y / av.getCharHeight() + av.getStartSeq(); - // chunkHeight = (da.getHeight() + 2)*charHeight; - // startx += chunkWidth; } else { @@ -160,125 +183,153 @@ public class SeqPanel extends JPanel if(seq>=av.getAlignment().getHeight()) return; - Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ; + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + if(res>sequence.getLength()) + return; + + Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ; String aa = ""; if(obj!=null) aa = obj.toString(); - StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName()); + StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName()); if(aa!="") text.append(" Residue: "+aa+" ("+ av.getAlignment().getSequenceAt(seq).findPosition(res)+")"); - parent.alignFrame.statusBar.setText(text.toString()); + ap.alignFrame.statusBar.setText(text.toString()); + + // use aa to see if the mouse pointer is on a + if( av.showSequenceFeatures) + { + Vector features = sequence.getSequenceFeatures(); + Enumeration e = features.elements(); + StringBuffer sbuffer = new StringBuffer(); + + + while (e.hasMoreElements()) + { + SequenceFeature sf = (SequenceFeature) e.nextElement(); + if (sf.getStart() <= sequence.findPosition(res) && + sf.getEnd() >= sequence.findPosition(res)) + { + if(sbuffer.length()>0) + sbuffer.append("; "); + sbuffer.append(sf.getType() + " " + sf.getDescription()); + if(sf.getStatus().length()>0) + sbuffer.append(" ("+sf.getStatus()+")"); + } + + } + + ToolTipManager.sharedInstance().registerComponent(this); + this.setToolTipText(sbuffer.toString()); + } + } public void doMouseDragged(MouseEvent evt) { // If we're dragging we're editing - editFlag = true; + + if(lastres==-1) + return; + int x = evt.getX(); int res = x/av.getCharWidth() + av.getStartRes(); - if (res < 0) {res = 0;} - - if (res != lastres) { - if (startseq != -1) { + if (res < 0) + res = 0; + if (res != lastres) + { // Group editing - if (av.getGroupEdit()) { - SequenceGroup sg = av.getAlignment().findGroup(startseq); - - if(sg!=null) - if (res < av.getAlignment().getWidth() && res < lastres) + if (evt.isAltDown() || evt.isControlDown()) + { + SequenceGroup sg = av.getSelectionGroup(); + if(sg==null) + av.getAlignment().findGroup(startseq); + if (sg != null) { - boolean flag = false; - for (int i= 0 ; i < sg.getSize(); i++) + boolean deleteAllowed = false; + if (res < av.getAlignment().getWidth() && res < lastres) { - SequenceI s = (SequenceI)sg.getSequenceAt(i); - for (int j=lastres-1; j >= res; j--) + /// Are we able to delete? + boolean allGaps = true; + for (int i = 0; i < sg.getSize(); i++) { - if (!flag) + SequenceI s = sg.getSequenceAt(i); + for (int j = lastres-1; j >= res && allGaps; j--) { - if (s.getSequence().charAt(j)!=av.getAlignment().getGapCharacter() && - s.getSequence().charAt(j)==' ') - { - res = j+1; - flag = true; - } - } - } - } - } - - if(sg!=null) - for (int i= 0 ; i < sg.getSize(); i++) - { - SequenceI s = (SequenceI)sg.getSequenceAt(i); - boolean found = false; - int sno = -1; - for (int k = 0; k < av.getAlignment().getHeight(); k++) - { - if (av.getAlignment().getSequenceAt(k) == s) - { - found = true; - sno = k; - break; - } - } - if (found && sno != -1) { - if (res < av.getAlignment().getWidth() && res > lastres) - { - for (int j = lastres; j < res; j++) - insertChar(j,sno); + if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j))) + { + res = j + 1; + allGaps = false; + } + } - int index = av.getAlignment().findIndex(s); - if (index != -1) - drawChars(index,index+1,lastres); + if(!deleteAllowed && allGaps) + deleteAllowed = true; + } + } + // drag to right + if (res < av.getAlignment().getWidth() && res > lastres) + sg.setEndRes(sg.getEndRes() + 1); - } else if (res < av.getAlignment().getWidth() && res < lastres) - { - for (int j = res; j < lastres; j++) - { - deleteChar(j,res,sno); - startres = res; - } - int index = av.getAlignment().findIndex(s); - if (index != -1) - drawChars(index,index+1,res); + // drag to left + else if (deleteAllowed && res < av.getAlignment().getWidth() && + res < lastres) + sg.setEndRes(sg.getEndRes() - 1); - } - } - } - lastres = res; - } else { - if (res < av.getAlignment().getWidth() && res > lastres) { - // dragging to the right - for (int j = lastres; j < res; j++) - insertChar(j,startseq); + for (int i = 0; i < sg.getSize(); i++) + { + SequenceI s = sg.getSequenceAt(i); + int k = av.alignment.findIndex(s); - drawChars(startseq,startseq+1,lastres); + // drag to right + if (res < av.getAlignment().getWidth() && res > lastres) + for (int j = lastres; j < res; j++) + insertChar(j, k); - } else if (res < av.getAlignment().getWidth() && res < lastres) + // drag to left + else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres) + { + for (int j = res; j < lastres; j++) + { + deleteChar(j, k); + startres = res; + } + } + } + } + } + else /////Editing a single sequence/////////// + { + if (res < av.getAlignment().getWidth() && res > lastres) + { + // dragging to the right + for (int j = lastres; j < res; j++) + insertChar(j, startseq); + } + else if (res < av.getAlignment().getWidth() && res < lastres) { - // dragging to the left - for (int j = res; j < lastres; j++) { - deleteChar(j,res,startseq); - startres = res; - } - drawChars(startseq,startseq+1,res); + for (int j = res; j < lastres; j++) + { + deleteChar(j, startseq); + startres = res; + } } + } - } - lastres = res; + } + lastres = res; repaint(); - return; } public void drawChars(int seqstart, int seqend, int start) { @@ -288,63 +339,83 @@ public class SeqPanel extends JPanel public void insertChar(int j, int seq) { - av.getAlignment().getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); + av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); seqEditOccurred=seq; } - public void deleteChar(int j, int res, int seq) + public void deleteChar(int j, int seq) { - if (av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='.' || - av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)=='-' || - av.getAlignment().getSequenceAt(seq).getSequence().charAt(j)==' ' ) - { - av.getAlignment().getSequenceAt(seq).deleteCharAt(j); - } + if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j))) + av.alignment.getSequenceAt(seq).deleteCharAt(j); - av.getAlignment().getWidth(); + av.alignment.getWidth(); repaint(); seqEditOccurred=seq; + } void updateConservation(int i) { - Alignment al = (Alignment) av.getAlignment(); - SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i)); - if(sg==null || !(sg.cs instanceof ConservationColourScheme)) - return; + av.updateConservation(); + av.updateConsensus(); - Conservation c = sg.getConservation(); + ColourSchemeI cs = av.getGlobalColourScheme(); + if(cs instanceof ConservationColourScheme) + cs = ( (ConservationColourScheme) cs).cs; - c = new Conservation("All", al.cons, - ResidueProperties.propHash, 3, sg.sequences, 0, - al.getWidth()); - c.calculate(); - c.verdict(false, 100); - sg.setConservation(c); - ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; - ccs.conserve = c; - } + if(cs instanceof ClustalxColourScheme) + cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth()); + ap.alignFrame.changeColour(cs); + } + +////////////////////////////////////////// +/////Everything below this is for defining the boundary of the rubberband +////////////////////////////////////////// + int oldSeq = -1; public void doMousePressedDefineMode(MouseEvent evt) { int res = evt.getX()/av.getCharWidth() + av.getStartRes(); int seq = evt.getY()/av.getCharHeight() + av.getStartSeq(); + oldSeq = seq; + + SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); + + if(sequence==null || res>sequence.getLength()) + return; + + stretchGroup = av.getSelectionGroup(); - stretchGroup = av.getRubberbandGroup(); if(stretchGroup == null) - stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq)); - else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq)) - || stretchGroup.getStartRes()res) { - System.out.println(stretchGroup.getStartRes()+" "+stretchGroup.getEndRes()+" "+res); - stretchGroup = null; + stretchGroup = av.alignment.findGroup( sequence ); + if(stretchGroup!=null && res>stretchGroup.getStartRes() && resres + || stretchGroup.getEndRes()= res) + { + stretchGroup = allGroups[i]; + av.setSelectionGroup(stretchGroup); + break; + } + } if(stretchGroup==null) { @@ -352,30 +423,34 @@ public class SeqPanel extends JPanel SequenceGroup sg = new SequenceGroup(); sg.setStartRes(res); sg.setEndRes(res); - sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) ); - av.setRubberbandGroup( sg ); + sg.addSequence( sequence ); + av.setSelectionGroup( sg ); stretchGroup = sg; - System.out.println("new rubberband group"); + + if(av.getConservationSelected()) + SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background"); + if(av.getAbovePIDThreshold()) + SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background"); + } else if( javax.swing.SwingUtilities.isRightMouseButton(evt)) { - // edit the properties of existing group + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null); + pop.show(this, evt.getX(), evt.getY()); + + // edit the properties of existing group } if(stretchGroup!=null && stretchGroup.getEndRes()==res) - { // Edit end res position of selected group changeEndRes = true; - } - if(stretchGroup!=null && stretchGroup.getStartRes()==res) - { + + else if(stretchGroup!=null && stretchGroup.getStartRes()==res) // Edit end res position of selected group changeStartRes = true; - } - seqCanvas.paintFlag = true; - repaint(); + repaint(); } @@ -385,21 +460,66 @@ public class SeqPanel extends JPanel boolean changeStartRes = false; SequenceGroup stretchGroup = null; - public void doMouseReleasedDefineMode(MouseEvent evt) { + mouseDragging = false; + + if(stretchGroup==null) + return; + + if(stretchGroup.cs instanceof ClustalxColourScheme) + { + stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth()); + repaint(); + } + + else if(stretchGroup.cs instanceof ConservationColourScheme) + { + ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs; + stretchGroup.cs = ccs; + SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ; + + repaint(); + } + else + { + if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold()) + { + ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs; + SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName()); + } + + } + + changeEndRes = false; changeStartRes = false; stretchGroup = null; + ap.idPanel.repaint(); } + + boolean remove = false; public void doMouseDraggedDefineMode(MouseEvent evt) { int res = evt.getX()/av.getCharWidth() + av.getStartRes(); - Sequence seq = (Sequence)av.getAlignment().getSequenceAt( - evt.getY()/av.getCharHeight() + av.getStartSeq()); + int y = evt.getY()/av.getCharHeight() + av.getStartSeq(); + + if(stretchGroup==null) + return; + + if(res>av.alignment.getWidth()) + res = av.alignment.getWidth()-1; + + + if(stretchGroup.getEndRes()==res) + // Edit end res position of selected group + changeEndRes = true; + + else if(stretchGroup.getStartRes()==res) + // Edit start res position of selected group + changeStartRes = true; - // SequenceGroup newSeqGroup = av.alignment.findGroup(seq); if(res oldSeq) + dragDirection = 1; + else if (y < oldSeq) + dragDirection = -1; + + while (y != oldSeq && oldSeq>0 && y 0) + running = ap.scrollUp(true); + + if (mouseDragging && evt.getY() >= getHeight() && + av.alignment.getHeight() > av.getEndSeq()) + running = ap.scrollUp(false); + + if (mouseDragging && evt.getX() < 0) + running = ap.scrollRight(true); + + else if (mouseDragging && evt.getX() >= getWidth()) + running = ap.scrollRight(false); + } + + try + { + Thread.sleep(75); + } + catch (Exception ex) + {} + } + } +} + + }