X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=ed9ce8d020e14d2ae5a58508aaffa3df22b0030c;hb=ad35f232acd499d9457056ca24b663866a09edd2;hp=d081f162aa91861e9e285bcf5d61ce9ffaed934d;hpb=f0ea7e292e26e7cec19720be39b143d261f53821;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index d081f16..ed9ce8d 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -19,13 +19,13 @@ package jalview.gui; import jalview.datamodel.*; - +import jalview.commands.EditCommand; import jalview.schemes.*; import java.awt.*; import java.awt.event.*; - import javax.swing.*; +import java.util.Vector; /** @@ -38,72 +38,78 @@ public class SeqPanel extends JPanel implements MouseListener, MouseMotionListener, MouseWheelListener { - /** DOCUMENT ME!! */ - public SeqCanvas seqCanvas; - - /** DOCUMENT ME!! */ - public AlignmentPanel ap; - protected int lastres; - protected int startseq; - protected AlignViewport av; - - // if character is inserted or deleted, we will need to recalculate the conservation - boolean seqEditOccurred = false; - ScrollThread scrollThread = null; - boolean mouseDragging = false; - boolean editingSeqs = false; - boolean groupEditing = false; - - ////////////////////////////////////////// - /////Everything below this is for defining the boundary of the rubberband - ////////////////////////////////////////// - int oldSeq = -1; - boolean changeEndSeq = false; - boolean changeStartSeq = false; - boolean changeEndRes = false; - boolean changeStartRes = false; - SequenceGroup stretchGroup = null; - boolean remove = false; - - Point lastMousePress; - boolean mouseWheelPressed = false; - StringBuffer keyboardNo1; - StringBuffer keyboardNo2; - - /** - * Creates a new SeqPanel object. - * - * @param avp DOCUMENT ME! - * @param p DOCUMENT ME! - */ - public SeqPanel(AlignViewport avp, AlignmentPanel p) + /** DOCUMENT ME!! */ + public SeqCanvas seqCanvas; + + /** DOCUMENT ME!! */ + public AlignmentPanel ap; + 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; + + StringBuffer tooltipText = new StringBuffer(""); + String tmpString; + + EditCommand editCommand; + + /** + * Creates a new SeqPanel object. + * + * @param avp DOCUMENT ME! + * @param p DOCUMENT ME! + */ + public SeqPanel(AlignViewport avp, AlignmentPanel p) + { + linkImageURL = getClass().getResource("/images/link.gif"); + ToolTipManager.sharedInstance().registerComponent(this); + ToolTipManager.sharedInstance().setInitialDelay(0); + ToolTipManager.sharedInstance().setDismissDelay(10000); + this.av = avp; + setBackground(Color.white); + + seqCanvas = new SeqCanvas(avp); + setLayout(new BorderLayout()); + add(seqCanvas, BorderLayout.CENTER); + + ap = p; + + if (!av.isDataset()) { - ToolTipManager.sharedInstance().registerComponent(this); - ToolTipManager.sharedInstance().setInitialDelay(0); - ToolTipManager.sharedInstance().setDismissDelay(10000); - this.av = avp; - setBackground(Color.white); - - seqCanvas = new SeqCanvas(avp); - setLayout(new BorderLayout()); - add(seqCanvas, BorderLayout.CENTER); - - ap = p; - - if(!av.isDataset()) - { - addMouseMotionListener(this); - addMouseListener(this); - addMouseWheelListener(this); - } + addMouseMotionListener(this); + addMouseListener(this); + addMouseWheelListener(this); } + } - int startWrapBlock=-1; - int wrappedBlock=-1; - int findRes(MouseEvent evt) - { - int res = 0; - int x = evt.getX(); + int startWrapBlock = -1; + int wrappedBlock = -1; + int findRes(MouseEvent evt) + { + int res = 0; + int x = evt.getX(); if (av.wrapAlignment) { @@ -115,67 +121,128 @@ public class SeqPanel extends JPanel implements MouseListener, int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + seqCanvas.getAnnotationHeight(); - int y = evt.getY(); - y -= hgap; - x -= seqCanvas.LABEL_WEST; - + int y = evt.getY(); + y -= hgap; + x -= seqCanvas.LABEL_WEST; - int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); + int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); + if (cwidth < 1) + return 0; - wrappedBlock = y / cHeight; - wrappedBlock += av.getStartRes() / cwidth; + wrappedBlock = y / cHeight; + wrappedBlock += av.getStartRes() / cwidth; - res = wrappedBlock * cwidth + x / av.getCharWidth(); + res = wrappedBlock * cwidth + x / av.getCharWidth(); } else { - res = (x / av.getCharWidth()) + av.getStartRes(); + res = (x / av.getCharWidth()) + av.getStartRes(); } - if(av.hasHiddenColumns) - res = av.getColumnSelection().adjustForHiddenColumns(res); + if (av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); return res; - } + } - int findSeq(MouseEvent evt) - { + int findSeq(MouseEvent evt) + { + int seq = 0; + int y = evt.getY(); - int seq = 0; - int y = evt.getY(); + if (av.wrapAlignment) + { + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; - if (av.wrapAlignment) - { - int hgap = av.charHeight; - if (av.scaleAboveWrapped) - hgap += av.charHeight; + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); + + y -= hgap; - int cHeight = av.getAlignment().getHeight() * av.charHeight - + hgap + seqCanvas.getAnnotationHeight(); + seq = Math.min( (y % cHeight) / av.getCharHeight(), + av.alignment.getHeight() - 1); + } + else + { + seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(), + av.alignment.getHeight() - 1); + } - y -= hgap; + return seq; + } - seq = ( (y % cHeight) / av.getCharHeight()); - } - else + SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res) + { + Vector tmp = new Vector(); + SequenceFeature[] features = sequence.getSequenceFeatures(); + if (features != null) + { + for (int i = 0; i < features.length; i++) + { + if (av.featuresDisplayed == null + || !av.featuresDisplayed.containsKey(features[i].getType())) + continue; + + if ( (features[i].getBegin() <= res) && + (features[i].getEnd() >= res)) + { + tmp.addElement(features[i]); + } + } + } + + features = new SequenceFeature[tmp.size()]; + for(int i=0; i= res) + { + if (av.featuresDisplayed.containsKey(sf.getType())) + { + allFeatures.addElement(sf); + } + } + index++; + } } - - return seq; - } + return allFeatures; + } void endEditing() { + if (editCommand!=null && editCommand.getSize() > 0) + { + ap.alignFrame.addHistoryItem(editCommand); + av.firePropertyChange("alignment", null, + av.getAlignment().getSequences()); + } + startseq = -1; lastres = -1; - seqEditOccurred = false; editingSeqs = false; groupEditing = false; keyboardNo1 = null; keyboardNo2 = null; + editCommand = null; } void setCursorRow() @@ -219,6 +286,25 @@ public class SeqPanel extends JPanel implements MouseListener, { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; + if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX)) + { + int original = seqCanvas.cursorX - dx; + int maxWidth = av.alignment.getWidth(); + + while(!av.colSel.isVisible(seqCanvas.cursorX) + && seqCanvas.cursorX0) + { + seqCanvas.cursorX += dx; + } + + if(seqCanvas.cursorX>=maxWidth + || !av.colSel.isVisible(seqCanvas.cursorX) ) + { + seqCanvas.cursorX = original; + } + } + scrollToVisible(); } @@ -252,12 +338,12 @@ public class SeqPanel extends JPanel implements MouseListener, } if (!av.wrapAlignment) { - while (seqCanvas.cursorX < av.startRes) + while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes)) { if (!ap.scrollRight(false)) break; } - while (seqCanvas.cursorX > av.endRes) + while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes)) { if (!ap.scrollRight(true)) break; @@ -316,7 +402,7 @@ public class SeqPanel extends JPanel implements MouseListener, else { // Now add any sequences between min and max - sg.sequences.clear(); + sg.getSequences(null).clear(); for (int i = min; i < max; i++) { sg.addSequence(av.alignment.getSequenceAt(i), false); @@ -339,24 +425,20 @@ public class SeqPanel extends JPanel implements MouseListener, void insertGapAtCursor(boolean group) { - ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", - av.alignment, HistoryItem.EDIT)); groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1)); - editOccurred(); + endEditing(); } void deleteGapAtCursor(boolean group) { - ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", - av.alignment, HistoryItem.EDIT)); groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1); editSequence(false, seqCanvas.cursorX); - editOccurred(); + endEditing(); } void numberPressed(char value) @@ -395,9 +477,8 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - editOccurred(); - endEditing(); + ap.repaint(); } @@ -433,17 +514,12 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - - int seq = findSeq(evt); int res = findRes(evt); if(seq<0 || res<0) return; - ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", - av.alignment, HistoryItem.EDIT)); - if ((seq < av.getAlignment().getHeight()) && (res < av.getAlignment().getSequenceAt(seq).getLength())) { @@ -494,67 +570,127 @@ public class SeqPanel extends JPanel implements MouseListener, setStatusMessage(sequence, res, seq); + + + tooltipText.setLength(6); // Cuts the buffer back to + + SequenceGroup [] groups = av.alignment.findAllGroups(sequence); + if(groups!=null) + { + for(int g=0; g=res) + { + if (!groups[g].getName().startsWith("JTreeGroup") && + !groups[g].getName().startsWith("JGroup")) + tooltipText.append(groups[g].getName() + " "); + + if(groups[g].getDescription()!=null) + tooltipText.append(groups[g].getDescription()+"
"); + } + } + } + + // use aa to see if the mouse pointer is on a if (av.showSequenceFeatures) { - SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures(); - if(features!=null) - { - StringBuffer sbuffer = new StringBuffer(""); + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), sequence.findPosition(res)); - for (int i = 0; i < features.length; i++) + if (features != null) + { + for (int i = 0; i < features.length; i++) + { + if (features[i].getType().equals("disulfide bond")) { - - if ( (features[i].getBegin() <= sequence.findPosition(res)) && - (features[i].getEnd() >= sequence.findPosition(res))) + if (features[i].getBegin() == sequence.findPosition(res) + || features[i].getEnd() == sequence.findPosition(res)) { - if(av.featuresDisplayed==null - || !av.featuresDisplayed.containsKey(features[i].getType())) - continue; + if (tooltipText.length() > 6) + tooltipText.append("
"); + tooltipText.append("disulfide bond " + features[i].getBegin() + ":" + + features[i].getEnd()); + if (features[i].links != null) + tooltipText.append(" "); + } + } + else + { + if (tooltipText.length() > 6) + tooltipText.append("
"); + tooltipText.append(features[i].getType() + " " + + features[i].begin); + if (features[i].begin != features[i].end) + tooltipText.append(" " + features[i].end); - if (features[i].getType().equals("disulfide bond")) + if (features[i].getDescription() != null + && !features[i].description.equals(features[i].getType())) + { + tmpString = features[i].getDescription(); + int startTag = tmpString.toUpperCase().indexOf(""); + if (startTag > -1) { - if (features[i].getBegin() == sequence.findPosition(res) - || features[i].getEnd() == sequence.findPosition(res)) - { - if (sbuffer.length() > 6) - sbuffer.append("
"); - sbuffer.append("disulfide bond " + features[i].getBegin() + ":" + - features[i].getEnd()); - } + tmpString = tmpString.substring(startTag + 6); } - else + int endTag = tmpString.toUpperCase().indexOf(""); + if (endTag > -1) + { + tmpString = tmpString.substring(0, endTag); + } + endTag = tmpString.toUpperCase().indexOf(""); + if (endTag > -1) { - if (sbuffer.length() > 6) - sbuffer.append("
"); - if(features[i].featureGroup!=null) - sbuffer.append(features[i].featureGroup+";"); + tmpString = tmpString.substring(0, endTag); + } - sbuffer.append(features[i].getType()); + if (startTag > -1) + { + tooltipText.append("; " + tmpString); + } + else + { + if (tmpString.indexOf("<") > -1 || tmpString.indexOf(">") > -1) + { + //The description does not specify html is to + //be used, so we must remove < > symbols + tmpString = tmpString.replaceAll("<", "<"); + tmpString = tmpString.replaceAll(">", ">"); - if (features[i].getDescription() != null - && !features[i].description.equals(features[i].getType())) - sbuffer.append("; " + features[i].getDescription()); + tooltipText.append("; "); + tooltipText.append(tmpString); - if (features[i].getStatus() != null && features[i].getStatus().length()>0) - { - sbuffer.append("; (" + features[i].getStatus() + ")"); } + else + tooltipText.append("; " + tmpString); } } + if (features[i].getValue("status") != null) + { + String status = features[i].getValue("status").toString(); + if (status.length() > 0) + tooltipText.append("; (" + features[i].getValue("status") + ")"); + } - } + if (features[i].links != null) + tooltipText.append(" "); - sbuffer.append(""); - if(sbuffer.length()==13) // - setToolTipText(""); - else - setToolTipText(sbuffer.toString()); + } } - else - setToolTipText(""); + } } + if (tooltipText.length() == 6) // + { + setToolTipText(null); + } + else + { + tooltipText.append(""); + setToolTipText(tooltipText.toString()); + } + // else + // setToolTipText(null); } void setStatusMessage(SequenceI sequence, int res, int seq) @@ -597,48 +733,48 @@ 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()10) + label = label.substring(0,10); + if(editCommand==null) + editCommand = new EditCommand("Edit "+label); + } if(insertGap) message.append(" insert "); @@ -715,10 +862,17 @@ public class SeqPanel extends JPanel implements MouseListener, //Are we editing within a selection group? if (groupEditing - || (sg != null && sg.sequences.contains(seq))) + || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq))) { fixedColumns = true; + //sg might be null as the user may only see 1 sequence, + //but the sequence represents a group + if (sg == null) + { + sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + } + fixedLeft = sg.getStartRes(); fixedRight = sg.getEndRes(); @@ -744,64 +898,52 @@ public class SeqPanel extends JPanel implements MouseListener, } - - if(av.hasHiddenColumns) - { - fixedColumns = true; - int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); - int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); - - if( ( insertGap && startres>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) + { + Vector vseqs = sg.getSequences(av.hiddenRepSequences); + int g, groupSize = vseqs.size(); + SequenceI[] groupSeqs = new SequenceI[groupSize]; + for (g = 0; g < groupSeqs.length; g++) + groupSeqs[g] = (SequenceI) vseqs.elementAt(g); // drag to right if (insertGap) { //If the user has selected the whole sequence, and is dragging to // the right, we can still extend the alignment and selectionGroup - if(sg.getStartRes() == 0 && sg.getEndRes() + 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(); @@ -816,13 +958,13 @@ public class SeqPanel extends JPanel implements MouseListener, fixedRight--) { blank = true; - for (int s = 0; s < sg.getSize(); s++) + + for (g = 0; g < groupSize; g++) { - seq = sg.getSequenceAt(s); for (int j = 0; j < startres - lastres; j++) { if (!jalview.util.Comparison.isGap( - seq.getCharAt(fixedRight - j))) + groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; @@ -835,12 +977,26 @@ public class SeqPanel extends JPanel implements MouseListener, if (!blank) { - if(sg.getSize() == av.alignment.getHeight()) + if(sg.getSize() == 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 { @@ -857,19 +1013,17 @@ 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 (g = 0; g < groupSize; g++) { - seq = sg.getSequenceAt(s); - for (int j = startres; j < lastres; j++) { - if (seq.getSequence().length() <= j) + if (groupSeqs[g].getLength() <= j) { continue; } if (!jalview.util.Comparison.isGap( - seq.getSequence().charAt(j))) + groupSeqs[g].getCharAt(j))) { // Not a gap, block edit not valid endEditing(); @@ -879,79 +1033,100 @@ public class SeqPanel extends JPanel implements MouseListener, } } - - for (int i = 0; i < sg.getSize(); i++) - { - seq = sg.getSequenceAt(i); - if (insertGap) { // dragging to the right - for (int j = lastres; j < startres; j++) + if (fixedColumns && fixedRight != -1) { - if (fixedColumns && fixedRight != -1) + for (int j = lastres; j < startres; j++) { - insertChar(j, seq, fixedRight); + insertChar(j, groupSeqs, fixedRight); } - else - insertChar(j, seq); + } + else + { + editCommand.appendEdit(EditCommand.INSERT_GAP, + groupSeqs, + startres, startres-lastres, + av.alignment, + true); } } else { // dragging to the left - for (int j = lastres; j > startres; j--) + if (fixedColumns && fixedRight != -1) { - if (fixedColumns && fixedRight != -1) - { - deleteChar(startres, seq, fixedRight); - } - else + for (int j = lastres; j > startres; j--) { - deleteChar(startres, seq); + deleteChar(startres, groupSeqs, fixedRight); } } + else + editCommand.appendEdit(EditCommand.DELETE_GAP, + groupSeqs, + startres, lastres - startres, + av.alignment, + true); + } - } } else /////Editing a single sequence/////////// { if (insertGap) { // dragging to the right - for (int j = lastres; j < startres; j++) + if (fixedColumns && fixedRight != -1) { - if (fixedColumns && fixedRight != -1) + for (int j = lastres; j < startres; j++) { - 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); + insertChar(j, new SequenceI[]{seq}, fixedRight); } - else - insertChar(j, seq); + } + else + { + editCommand.appendEdit(EditCommand.INSERT_GAP, + new SequenceI[] + {seq}, + lastres, startres-lastres, + av.alignment, + true); } } else { // dragging to the left - for (int j = lastres; j > startres; j--) + if (fixedColumns && fixedRight != -1) { - if (fixedColumns && fixedRight != -1) + for (int j = lastres; j > startres; j--) { - deleteChar(startres, seq, fixedRight); + if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) + { + endEditing(); + break; + } + deleteChar(startres, new SequenceI[]{seq}, fixedRight); } - else + } + else + { + //could be a keyboard edit trying to delete none gaps + int max=0; + for(int m = startres; m0) { - deleteChar(startres, seq); + editCommand.appendEdit(EditCommand.DELETE_GAP, + new SequenceI[] + {seq}, + startres, max, + av.alignment, + true); } } } @@ -962,83 +1137,55 @@ public class SeqPanel extends JPanel implements MouseListener, } - /** - * DOCUMENT ME! - * - * @param j DOCUMENT ME! - * @param seq DOCUMENT ME! - */ - void insertChar(int j, SequenceI seq) - { - seq.insertCharAt(j, av.getGapCharacter()); - seqEditOccurred = true; - } - void insertChar(int j, SequenceI seq, int fixedColumn) + void insertChar(int j, SequenceI [] seq, int fixedColumn) { - //Find the next gap before the end of the visible region boundary - //If lastCol > j, theres a boundary after the gap insertion int blankColumn = fixedColumn; - for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) + for(int s=0; s j, theres a boundary after the gap insertion + + for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) { - //Theres a space, so break and insert the gap - break; + if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn))) + { + //Theres a space, so break and insert the gap + break; + } } - } - if (blankColumn <= j) - { - endEditing(); - return; + if (blankColumn <= j) + { + blankColumn = fixedColumn; + endEditing(); + return; + } } - if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn))) - { - //Just Checking - System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn)); - return; - } + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + blankColumn, 1, av.alignment, true); - seq.deleteCharAt(blankColumn); - seq.insertCharAt(j, av.getGapCharacter()); - seqEditOccurred = true; - } + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + j, 1, av.alignment, + true); - void deleteChar(int j, SequenceI seq, int fixedColumn) - { - if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) - { - ap.alignFrame.statusBar.setText( - "End editing: Tried removing residue " + seq.getCharAt(j)); - return; - } - - seq.deleteCharAt(j); - seq.insertCharAt(fixedColumn, av.getGapCharacter()); - seqEditOccurred = true; } - /** - * DOCUMENT ME! - * - * @param j DOCUMENT ME! - * @param seq DOCUMENT ME! - */ - void deleteChar(int j, SequenceI seq) + void deleteChar(int j, SequenceI [] seq, int fixedColumn) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) - { - ap.alignFrame.statusBar.setText( - "End editing: Tried removing residue " + seq.getCharAt(j)); - return; - } - seq.deleteCharAt(j); - seqEditOccurred = true; - seqCanvas.repaint(); + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + j, 1, av.alignment, true); + + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + fixedColumn, 1, av.alignment, true); } + /** * DOCUMENT ME! * @@ -1075,7 +1222,38 @@ public class SeqPanel extends JPanel implements MouseListener, } public void mouseClicked(MouseEvent evt) - {} + { + SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) ); + if(evt.getClickCount()>1) + { + if (av.getSelectionGroup().getSize() == 1 + && av.getSelectionGroup().getEndRes() + - av.getSelectionGroup().getStartRes() < 2) + av.setSelectionGroup(null); + + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), + sequence.findPosition( findRes(evt) ) + ); + + if(features!=null && features.length>0) + { + SearchResults highlight = new SearchResults(); + highlight.addResult(sequence, + features[0].getBegin(), + features[0].getEnd()); + seqCanvas.highlightSearchResults(highlight); + } + if(features!=null && features.length>0) + { + seqCanvas.getFeatureRenderer().amendFeatures( + new SequenceI[] + {sequence}, features, false, ap); + + seqCanvas.highlightSearchResults(null); + } + } + } public void mouseWheelMoved(MouseWheelEvent e) { @@ -1106,26 +1284,6 @@ public class SeqPanel extends JPanel implements MouseListener, } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - */ - void editOccurred() - { - if (!seqEditOccurred) - { - ap.alignFrame.historyList.pop(); - ap.alignFrame.updateEditMenuBar(); - } - - endEditing(); - - av.firePropertyChange("alignment", null,av.getAlignment().getSequences()); - - } - /** * DOCUMENT ME! * @@ -1145,7 +1303,7 @@ 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 +1332,7 @@ public class SeqPanel extends JPanel implements MouseListener, stretchGroup = null; } } - else if (!stretchGroup.sequences.contains(sequence) || + else if (!stretchGroup.getSequences(null).contains(sequence) || (stretchGroup.getStartRes() > res) || (stretchGroup.getEndRes() < res)) { @@ -1190,12 +1348,36 @@ 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 +1388,44 @@ 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(); } @@ -1270,16 +1446,21 @@ public class SeqPanel extends JPanel implements MouseListener, { if (stretchGroup.cs instanceof ClustalxColourScheme) { - ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup. - sequences, + ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX( + stretchGroup.getSequences(av.hiddenRepSequences), stretchGroup.getWidth()); } + if (stretchGroup.cs instanceof Blosum62ColourScheme + || stretchGroup.cs instanceof PIDColourScheme + || stretchGroup.cs.conservationApplied() + || stretchGroup.cs.getThreshold()>0) + stretchGroup.recalcConservation(); + if (stretchGroup.cs.conservationApplied()) { SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()); - stretchGroup.recalcConservation(); } else { @@ -1290,7 +1471,8 @@ public class SeqPanel extends JPanel implements MouseListener, changeEndRes = false; changeStartRes = false; stretchGroup = null; - PaintRefresher.Refresh(av.alignment); + + PaintRefresher.Refresh(this, av.getSequenceSetId()); } /** @@ -1311,12 +1493,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - - if(y > av.alignment.getHeight()) - { - y = av.alignment.getHeight() -1; - } - if(res> av.alignment.getWidth()) + if(res>= av.alignment.getWidth()) { res = av.alignment.getWidth()-1; } @@ -1377,7 +1554,7 @@ public class SeqPanel extends JPanel implements MouseListener, Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - if (stretchGroup.sequences.contains(nextSeq)) + if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); }