X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=a4d924073bbc11d04364c081b3d5e5b8f00135c6;hb=09d25d31d26bdc71914b8441872f724f1d75f0cc;hp=d081f162aa91861e9e285bcf5d61ce9ffaed934d;hpb=f0ea7e292e26e7cec19720be39b143d261f53821;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index d081f16..a4d9240 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -27,6 +27,8 @@ import java.awt.event.*; import javax.swing.*; +import java.util.Vector; + /** * DOCUMENT ME! @@ -70,6 +72,8 @@ public class SeqPanel extends JPanel implements MouseListener, StringBuffer keyboardNo1; StringBuffer keyboardNo2; + java.net.URL linkImageURL; + /** * Creates a new SeqPanel object. * @@ -78,6 +82,7 @@ public class SeqPanel extends JPanel implements MouseListener, */ public SeqPanel(AlignViewport avp, AlignmentPanel p) { + linkImageURL = getClass().getResource("/images/link.gif"); ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -142,7 +147,6 @@ public class SeqPanel extends JPanel implements MouseListener, int findSeq(MouseEvent evt) { - int seq = 0; int y = evt.getY(); @@ -157,16 +161,41 @@ public class SeqPanel extends JPanel implements MouseListener, y -= hgap; - seq = ( (y % cHeight) / av.getCharHeight()); + seq = Math.min( (y % cHeight) / av.getCharHeight(), + av.alignment.getHeight() -1); } else { - seq = (y / av.getCharHeight()) + av.getStartSeq(); + seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(), + av.alignment.getHeight() -1); } return seq; } + Vector getAllFeaturesAtRes(SequenceI seq, int res) + { + Vector allFeatures = new Vector(); + int index = 0; + if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null) + { + while (index < seq.getSequenceFeatures().length) + { + SequenceFeature sf = seq.getSequenceFeatures()[index]; + if (sf.getBegin() <= res && + sf.getEnd() >= res) + { + if (av.featuresDisplayed.containsKey(sf.getType())) + { + allFeatures.addElement(sf); + } + } + index++; + } + } + return allFeatures; + } + void endEditing() { startseq = -1; @@ -280,7 +309,7 @@ public class SeqPanel extends JPanel implements MouseListener, SequenceGroup sg = av.selectionGroup; //Find the top and bottom of this group int min = av.alignment.getHeight(), max = 0; - for(int i=0; i max) @@ -316,7 +345,7 @@ public class SeqPanel extends JPanel implements MouseListener, else { // Now add any sequences between min and max - sg.sequences.clear(); + sg.getSequences(false).clear(); for (int i = min; i < max; i++) { sg.addSequence(av.alignment.getSequenceAt(i), false); @@ -397,7 +426,6 @@ public class SeqPanel extends JPanel implements MouseListener, editOccurred(); - endEditing(); ap.repaint(); } @@ -501,6 +529,7 @@ public class SeqPanel extends JPanel implements MouseListener, if(features!=null) { StringBuffer sbuffer = new StringBuffer(""); + StringBuffer seqSpecific = new StringBuffer(); for (int i = 0; i < features.length; i++) { @@ -522,30 +551,46 @@ public class SeqPanel extends JPanel implements MouseListener, sbuffer.append("
"); sbuffer.append("disulfide bond " + features[i].getBegin() + ":" + features[i].getEnd()); + if (features[i].links != null) + sbuffer.append(" "); } } else { if (sbuffer.length() > 6) sbuffer.append("
"); - if(features[i].featureGroup!=null) - sbuffer.append(features[i].featureGroup+";"); - sbuffer.append(features[i].getType()); + sbuffer.append(features[i].getType() + " " + + features[i].begin); + if (features[i].begin != features[i].end) + sbuffer.append(" " + features[i].end); if (features[i].getDescription() != null && !features[i].description.equals(features[i].getType())) sbuffer.append("; " + features[i].getDescription()); - if (features[i].getStatus() != null && features[i].getStatus().length()>0) + if (features[i].getValue("status") != null) { - sbuffer.append("; (" + features[i].getStatus() + ")"); + sbuffer.append("; (" + features[i].getValue("status") + ")"); } + if (features[i].links != null) + sbuffer.append(" "); + } } + else if(features[i].begin==0 && features[i].end==0) + { + // seqSpecific.append(features[i].featureGroup+": " + // + features[i].getType()+" " + // +features[i].getDescription()+"
"); + } } + if(seqSpecific.length()>0) + seqSpecific.setLength(seqSpecific.length()-4); + + sbuffer.append(seqSpecific); sbuffer.append(""); if(sbuffer.length()==13) // setToolTipText(""); @@ -597,48 +642,48 @@ public class SeqPanel extends JPanel implements MouseListener, */ public void mouseDragged(MouseEvent evt) { - if(mouseWheelPressed) + if (mouseWheelPressed) { int oldWidth = av.charWidth; //Which is bigger, left-right or up-down? - if( Math.abs(evt.getY()-lastMousePress.getY()) - > Math.abs(evt.getX()-lastMousePress.getX())) - { - int fontSize = av.font.getSize(); - - if (evt.getY() < lastMousePress.getY() && av.charHeight > 1) - { - fontSize--; - } - else if (evt.getY() > lastMousePress.getY()) - { - fontSize++; - } + if (Math.abs(evt.getY() - lastMousePress.getY()) + > Math.abs(evt.getX() - lastMousePress.getX())) + { + int fontSize = av.font.getSize(); - av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); - av.charWidth = oldWidth; - ap.fontChanged(); + if (evt.getY() < lastMousePress.getY()) + { + fontSize--; + } + else if (evt.getY() > lastMousePress.getY()) + { + fontSize++; + } + if(fontSize<1) + fontSize = 1; - } - else - { - if (evt.getX() < lastMousePress.getX() && av.charWidth > 1) - { - av.charWidth--; - } - else if (evt.getX() > lastMousePress.getX()) - { - av.charWidth++; - } + av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); + av.charWidth = oldWidth; + ap.fontChanged(); + } + else + { + if (evt.getX() < lastMousePress.getX() && av.charWidth > 1) + { + av.charWidth--; + } + else if (evt.getX() > lastMousePress.getX()) + { + av.charWidth++; + } - ap.repaint(); - } + ap.repaint(); + } - FontMetrics fm = getFontMetrics(av.getFont()); - av.showText = (fm.charWidth('M') < av.charWidth); - // && fm.getHeight()y1 && lastresy2) ) - { - endEditing(); - return; - } - - if(fixedRightfixedLeft && fixedLeft==-1) - fixedLeft = y1; - } - - if (groupEditing) + if(av.hasHiddenColumns ) { + fixedColumns = true; + int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); + int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); - /*if (av.hasHiddenRows) - { - //sg might be null as the user may only see 1 sequence - if (sg == null) + if ( (insertGap && startres > y1 && lastres < y1) + || (!insertGap && startres < y2 && lastres > y2)) { - sg = new SequenceGroup(); - sg.addSequence(av.alignment.getSequenceAt(startseq), false); + endEditing(); + return; } - SequenceGroup tmp = new SequenceGroup(); - - //Do any of the sequences have hidden associates? - for (int s = 0; s < sg.getSize(); s++) + //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); + //Selection spans a hidden region + if(fixedLefty2 || fixedRight==-1)) { - seq = sg.getSequenceAt(s); - tmp.addSequence(seq, false); - if (seq.getHiddenSequences() != null) + if(startres>=y2) { - for (int h = 0; h < seq.getHiddenSequences().getSize(); h++) - tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h), - false); + fixedLeft = y2; } + else + { + fixedRight = y2 - 1; + } } - - sg = tmp; - }*/ - // int blankColumn = -1; + } + if (groupEditing) + { // drag to right if (insertGap) { //If the user has selected the whole sequence, and is dragging to // the right, we can still extend the alignment and selectionGroup - if(sg.getStartRes() == 0 && sg.getEndRes() + 1 == av.alignment.getWidth()) + if( sg.getStartRes() == 0 + && sg.getEndRes() == fixedRight + && sg.getEndRes() == av.alignment.getWidth()-1 + ) { sg.setEndRes(av.alignment.getWidth() + startres - lastres); fixedRight = sg.getEndRes(); @@ -816,9 +856,9 @@ public class SeqPanel extends JPanel implements MouseListener, fixedRight--) { blank = true; - for (int s = 0; s < sg.getSize(); s++) + for (int s = 0; s < sg.getSize(true); s++) { - seq = sg.getSequenceAt(s); + seq = (SequenceI)sg.getSequences(true).elementAt(s); for (int j = 0; j < startres - lastres; j++) { if (!jalview.util.Comparison.isGap( @@ -835,12 +875,26 @@ public class SeqPanel extends JPanel implements MouseListener, if (!blank) { - if(sg.getSize() == av.alignment.getHeight()) + if(sg.getSize(false) == av.alignment.getHeight() ) { + if((av.hasHiddenColumns + && startresalWidth) + alWidth = hwidth; + } //We can still insert gaps if the selectionGroup //contains all the sequences sg.setEndRes(sg.getEndRes()+startres-lastres); - fixedRight = av.alignment.getWidth()+startres-lastres; + fixedRight = alWidth+startres-lastres; } else { @@ -857,9 +911,9 @@ public class SeqPanel extends JPanel implements MouseListener, /// Are we able to delete? // ie are all columns blank? - for (int s = 0; s < sg.getSize(); s++) + for (int s = 0; s < sg.getSize(true); s++) { - seq = sg.getSequenceAt(s); + seq = (SequenceI)sg.getSequences(true).elementAt(s); for (int j = startres; j < lastres; j++) { @@ -880,9 +934,9 @@ public class SeqPanel extends JPanel implements MouseListener, } - for (int i = 0; i < sg.getSize(); i++) + for (int i = 0; i < sg.getSize(true); i++) { - seq = sg.getSequenceAt(i); + seq = (SequenceI) sg.getSequences(true).elementAt(i); if (insertGap) { @@ -923,17 +977,6 @@ public class SeqPanel extends JPanel implements MouseListener, { if (fixedColumns && fixedRight != -1) { - if (sg.getStartRes() == 0 - && sg.getEndRes() + 1 == av.alignment.getWidth() - && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight))) - { - //Single sequence edit, whole sequence selected, - //extend the selection group - sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres); - fixedColumns = false; - insertChar(j, seq); - } - else insertChar(j, seq, fixedRight); } else @@ -990,6 +1033,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (blankColumn <= j) { + blankColumn = fixedColumn; endEditing(); return; } @@ -1145,7 +1189,7 @@ public class SeqPanel extends JPanel implements MouseListener, "Cannot edit annotations in wrapped view.", "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE); - return; + return; } if(seq<0 || res<0) @@ -1174,7 +1218,7 @@ public class SeqPanel extends JPanel implements MouseListener, stretchGroup = null; } } - else if (!stretchGroup.sequences.contains(sequence) || + else if (!stretchGroup.getSequences(false).contains(sequence) || (stretchGroup.getStartRes() > res) || (stretchGroup.getEndRes() < res)) { @@ -1190,12 +1234,36 @@ public class SeqPanel extends JPanel implements MouseListener, (allGroups[i].getEndRes() >= res)) { stretchGroup = allGroups[i]; - av.setSelectionGroup(stretchGroup); - break; } } } + + av.setSelectionGroup(stretchGroup); + + } + + + if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + { + Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); + Vector links = new Vector(); + for (int i = 0; i < allFeatures.size(); i++) + { + SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i); + if (sf.links != null) + { + for (int j = 0; j < sf.links.size(); j++) + { + links.addElement(sf.links.elementAt(j)); + } + } + } + + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links); + pop.show(this, evt.getX(), evt.getY()); + return; } if (av.cursorMode) @@ -1206,50 +1274,44 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - 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"); - } + //Only if left mouse button do we want to change group sizes - if (av.getAbovePIDThreshold()) - { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); - } - } - else if (javax.swing.SwingUtilities.isRightMouseButton(evt)) - { - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null); - pop.show(this, evt.getX(), evt.getY()); + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; - // edit the properties of existing group - } + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, + av.getGlobalColourScheme(), + "Background"); + } - if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) - { + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), + "Background"); + } + if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res)) + { // Edit end res position of selected group changeEndRes = true; - } - else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) - { + } + else if ( (stretchGroup != null) && + (stretchGroup.getStartRes() == res)) + { // Edit end res position of selected group changeStartRes = true; + } + stretchGroup.getWidth(); } - stretchGroup.getWidth(); - seqCanvas.repaint(); } @@ -1270,8 +1332,8 @@ public class SeqPanel extends JPanel implements MouseListener, { if (stretchGroup.cs instanceof ClustalxColourScheme) { - ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup. - sequences, + ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX( + stretchGroup.getSequences(true), stretchGroup.getWidth()); } @@ -1311,11 +1373,6 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - - if(y > av.alignment.getHeight()) - { - y = av.alignment.getHeight() -1; - } if(res> av.alignment.getWidth()) { res = av.alignment.getWidth()-1; @@ -1377,7 +1434,7 @@ public class SeqPanel extends JPanel implements MouseListener, Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - if (stretchGroup.sequences.contains(nextSeq)) + if (stretchGroup.getSequences(false).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); }