X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=5782797d0f293619da66981c6fa36153a514fd64;hb=9ca1d7a3776d77e402c3899184ae041d56f72ca6;hp=2fe27b381bf84bffe35aac5fb94700b32ef764fa;hpb=02f2f19fdecb0b7afa5b61b07c56d46d40948674;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 2fe27b3..5782797 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 @@ -27,6 +27,8 @@ import java.awt.event.*; import javax.swing.*; +import java.util.Vector; + /** * DOCUMENT ME! @@ -45,8 +47,6 @@ public class SeqPanel extends JPanel implements MouseListener, public AlignmentPanel ap; protected int lastres; protected int startseq; - int startEdit = -1; - int endEdit = -1; protected AlignViewport av; // if character is inserted or deleted, we will need to recalculate the conservation @@ -67,7 +67,12 @@ public class SeqPanel extends JPanel implements MouseListener, SequenceGroup stretchGroup = null; boolean remove = false; + Point lastMousePress; boolean mouseWheelPressed = false; + StringBuffer keyboardNo1; + StringBuffer keyboardNo2; + + java.net.URL linkImageURL; /** * Creates a new SeqPanel object. @@ -77,6 +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); @@ -120,6 +126,8 @@ public class SeqPanel extends JPanel implements MouseListener, int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); + if(cwidth<1) + return 0; wrappedBlock = y / cHeight; wrappedBlock += av.getStartRes() / cwidth; @@ -141,7 +149,6 @@ public class SeqPanel extends JPanel implements MouseListener, int findSeq(MouseEvent evt) { - int seq = 0; int y = evt.getY(); @@ -156,16 +163,41 @@ 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; @@ -173,8 +205,211 @@ public class SeqPanel extends JPanel implements MouseListener, seqEditOccurred = false; editingSeqs = false; groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + } + + void setCursorRow() + { + seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } + + void setCursorColumn() + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } + + void setCursorRowAndColumn() + { + if(keyboardNo2==null) + { + keyboardNo2 = new StringBuffer(); + } + else + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; + seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1; + scrollToVisible(); + } + } + + void setCursorPosition() + { + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + + seqCanvas.cursorX = sequence.findIndex( + getKeyboardNo(keyboardNo1)-1 + ); + scrollToVisible(); + } + + void moveCursor(int dx, int dy) + { + seqCanvas.cursorX += dx; + seqCanvas.cursorY += dy; + scrollToVisible(); + } + + void scrollToVisible() + { + if (seqCanvas.cursorX < 0) + seqCanvas.cursorX = 0; + else if (seqCanvas.cursorX > av.alignment.getWidth() - 1) + seqCanvas.cursorX = av.alignment.getWidth() - 1; + + if (seqCanvas.cursorY < 0) + seqCanvas.cursorY = 0; + else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) + seqCanvas.cursorY = av.alignment.getHeight() - 1; + + + endEditing(); + if(av.wrapAlignment) + { + ap.scrollToWrappedVisible(seqCanvas.cursorX); + } + else + { + while (seqCanvas.cursorY < av.startSeq) + { + ap.scrollUp(true); + } + while (seqCanvas.cursorY + 1 > av.endSeq) + { + ap.scrollUp(false); + } + if (!av.wrapAlignment) + { + while (seqCanvas.cursorX < av.startRes) + { + if (!ap.scrollRight(false)) + break; + } + while (seqCanvas.cursorX > av.endRes) + { + if (!ap.scrollRight(true)) + break; + } + } + } + setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), + seqCanvas.cursorX, seqCanvas.cursorY); + + seqCanvas.repaint(); + } + + void setSelectionAreaAtCursor(boolean topLeft) + { + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + + if(av.getSelectionGroup()!=null) + { + SequenceGroup sg = av.selectionGroup; + //Find the top and bottom of this group + int min = av.alignment.getHeight(), max = 0; + for(int i=0; i max) + max = index; + if(index < min) + min = index; + } + + max ++; + + if(topLeft) + { + sg.setStartRes(seqCanvas.cursorX); + if(sg.getEndRes()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(false).clear(); + for (int i = min; i < max; i++) + { + sg.addSequence(av.alignment.getSequenceAt(i), false); + } + } + } + + if (av.getSelectionGroup() == null) + { + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(seqCanvas.cursorX); + sg.setEndRes(seqCanvas.cursorX); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + } + + + ap.repaint(); } + 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(); + } + + 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(); + } + + void numberPressed(char value) + { + if(keyboardNo1==null) + keyboardNo1 = new StringBuffer(); + + if(keyboardNo2!=null) + keyboardNo2.append(value); + else + keyboardNo1.append(value); + } + + int getKeyboardNo(StringBuffer kb) + { + if(kb==null) + return 1; + else + return Integer.parseInt(kb.toString()); + } + + /** * DOCUMENT ME! * @@ -183,6 +418,7 @@ public class SeqPanel extends JPanel implements MouseListener, public void mouseReleased(MouseEvent evt) { mouseDragging = false; + mouseWheelPressed = false; if (!editingSeqs) { @@ -190,13 +426,9 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - if (seqEditOccurred) - { - editOccurred(); - } + editOccurred(); - endEditing(); - ap.repaint(); + ap.repaint(); } @@ -208,6 +440,8 @@ public class SeqPanel extends JPanel implements MouseListener, */ public void mousePressed(MouseEvent evt) { + lastMousePress = evt.getPoint(); + if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) { mouseWheelPressed = true; @@ -230,8 +464,6 @@ public class SeqPanel extends JPanel implements MouseListener, } - ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", - av.alignment, HistoryItem.EDIT)); int seq = findSeq(evt); int res = findRes(evt); @@ -239,6 +471,9 @@ public class SeqPanel extends JPanel implements MouseListener, 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())) { @@ -251,9 +486,6 @@ public class SeqPanel extends JPanel implements MouseListener, lastres = -1; } - startEdit = lastres; - endEdit = lastres; - return; } @@ -274,6 +506,7 @@ public class SeqPanel extends JPanel implements MouseListener, int res = findRes(evt); int seq = findSeq(evt); + if(res<0 || seq<0 || seq >= av.getAlignment().getHeight()) return; @@ -289,36 +522,7 @@ public class SeqPanel extends JPanel implements MouseListener, seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); } - - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + - sequence.getName()); - - Object obj = null; - if (av.alignment.isNucleotide()) - { - obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + - ""); - if(obj!=null) - text.append(" Nucleotide: "); - } - else - { - obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); - if(obj!=null) - text.append(" Residue: "); - } - - if (obj != null) - { - - if (obj != "") - { - text.append( obj + " (" + - av.getAlignment().getSequenceAt(seq).findPosition(res) + ")"); - } - } - - ap.alignFrame.statusBar.setText(text.toString()); + setStatusMessage(sequence, res, seq); // use aa to see if the mouse pointer is on a if (av.showSequenceFeatures) @@ -327,6 +531,7 @@ 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++) { @@ -334,7 +539,8 @@ public class SeqPanel extends JPanel implements MouseListener, if ( (features[i].getBegin() <= sequence.findPosition(res)) && (features[i].getEnd() >= sequence.findPosition(res))) { - if(!av.featuresDisplayed.containsKey(features[i].getType())) + if(av.featuresDisplayed==null + || !av.featuresDisplayed.containsKey(features[i].getType())) continue; @@ -347,30 +553,46 @@ 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(""); @@ -382,6 +604,39 @@ public class SeqPanel extends JPanel implements MouseListener, } } + void setStatusMessage(SequenceI sequence, int res, int seq) + { + StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + + sequence.getName()); + + Object obj = null; + if (av.alignment.isNucleotide()) + { + obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + + ""); + if (obj != null) + text.append(" Nucleotide: "); + } + else + { + obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); + if (obj != null) + text.append(" Residue: "); + } + + if (obj != null) + { + + if (obj != "") + { + text.append(obj + " (" + sequence.findPosition(res) + + ")"); + } + } + ap.alignFrame.statusBar.setText(text.toString()); + + } + /** * DOCUMENT ME! * @@ -389,6 +644,54 @@ public class SeqPanel extends JPanel implements MouseListener, */ public void mouseDragged(MouseEvent evt) { + if (mouseWheelPressed) + { + int oldWidth = av.charWidth; + + //Which is bigger, left-right or up-down? + if (Math.abs(evt.getY() - lastMousePress.getY()) + > Math.abs(evt.getX() - lastMousePress.getX())) + { + int fontSize = av.font.getSize(); + + if (evt.getY() < lastMousePress.getY()) + { + fontSize--; + } + else if (evt.getY() > lastMousePress.getY()) + { + fontSize++; + } + + if(fontSize<1) + fontSize = 1; + + 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(); + } + + FontMetrics fm = getFontMetrics(av.getFont()); + av.validCharWidth = fm.charWidth('M') <= av.charWidth; + + lastMousePress = evt.getPoint(); + + return; + } + if (!editingSeqs) { doMouseDraggedDefineMode(evt); @@ -407,240 +710,383 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - boolean dragRight = true; - - if ((res < av.getAlignment().getWidth()) && (res < lastres)) + if ( (res < av.getAlignment().getWidth()) && (res < lastres)) { - dragRight = false; + // dragLeft, delete gap + editSequence(false, res); } - else if(av.hasHiddenColumns) + else + editSequence(true, res); + + mouseDragging = true; + if(scrollThread!=null) + scrollThread.setEvent(evt); + + } + + synchronized void editSequence(boolean insertGap, int startres) + { + int fixedLeft = -1; + int fixedRight = -1; + boolean fixedColumns = false; + SequenceGroup sg = av.getSelectionGroup(); + + + if (!groupEditing && av.hasHiddenRows) { - //Stop editing if the user has dragged beyond hiddenBoundary - int lastCol = av.getColumnSelection().getHiddenRegionBoundary(lastres); - if( lastCol < res) + if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null) { - if(lastres!=lastCol) - { - endEditing(); - return; - } + groupEditing = true; } } - if(!groupEditing && av.hasHiddenRows) + //No group, but the sequence may represent a group + if (groupEditing + && sg == null + && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null) { - if(av.alignment.getSequenceAt(startseq).getHiddenSequences()!=null) - { - groupEditing = true; - } + groupEditing = false; } + SequenceI seq = av.alignment.getSequenceAt(startseq); + StringBuffer message = new StringBuffer(); + if (groupEditing) + message.append("Edit group:"); + else + message.append("Edit sequence: "+seq.getName()); - if (res != lastres) - { - SequenceI seq; - // Group editing - if (groupEditing) - { - SequenceGroup sg = av.getSelectionGroup(); + if(insertGap) + message.append(" insert "); + else + message.append(" delete "); - if (av.hasHiddenRows) - { - //sg might be null as the user may only see 1 sequence - if(sg==null) - { - sg = new SequenceGroup(); - sg.addSequence(av.alignment.getSequenceAt(startseq), false); - } + message.append(Math.abs(startres-lastres)+" gaps."); + ap.alignFrame.statusBar.setText(message.toString()); - SequenceGroup tmp = new SequenceGroup(); - //Do any of the sequences have hidden associates? - for (int s = 0; s < sg.getSize(); s++) - { - seq = sg.getSequenceAt(s); - tmp.addSequence(seq, false); - if (seq.getHiddenSequences()!=null) - { - for(int h=0; h= fixedLeft) + || (startres >= fixedLeft && lastres < fixedLeft) + || (startres > fixedRight && lastres <=fixedRight) + || (startres <= fixedRight && lastres > fixedRight)) + { + endEditing(); + return; + } - int blankColumn = -1; + if (fixedLeft > startres) + { + fixedRight = fixedLeft - 1; + fixedLeft = 0; + } + else if (fixedRight < startres) + { + fixedLeft = fixedRight; + fixedRight = -1; + } + } - // drag to right - if (dragRight) - { - // Is it valid?? - // Find the next gap before the end - // of the visible region boundary - if (av.hasHiddenColumns) - { - if(res-lastres > 1) - { - res = lastres+1; - } + if(av.hasHiddenColumns ) + { + fixedColumns = true; + int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); + int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + if ( (insertGap && startres > y1 && lastres < y1) + || (!insertGap && startres < y2 && lastres > y2)) + { + endEditing(); + return; + } - int lastCol = av.getColumnSelection(). - getHiddenRegionBoundary(res); + //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); + //Selection spans a hidden region + if(fixedLefty2 || fixedRight==-1)) + { + if(startres>=y2) + { + fixedLeft = y2; + } + else + { + fixedRight = y2 - 1; + } + } + } - if(lastCol!=res) - { - for (blankColumn = lastCol; - blankColumn > lastres; - blankColumn--) - { - boolean blank = true; - for (int s = 0; s < sg.getSize(); s++) - { - seq = sg.getSequenceAt(s); - - if (seq.getSequence().length() <= blankColumn) - { - continue; - } - - if (!jalview.util.Comparison.isGap( - seq.getSequence().charAt(blankColumn))) - { - blank = false; - continue; - } - } - if (blank) - break; - } - - - if (blankColumn <= lastres) - { - endEditing(); - return; - } - } - else - blankColumn = -1; + if (groupEditing) + { + Vector vseqs = sg.getSequences(true); + int g, groupSize = vseqs.size(); + SequenceI[] groupSeqs = new SequenceI[groupSize]; + for (g = 0; g < groupSeqs.length; g++) + groupSeqs[g] = (SequenceI) vseqs.elementAt(g); + + // drag to right + if (insertGap) + { + //If the user has selected the whole sequence, and is dragging to + // the right, we can still extend the alignment and selectionGroup + if( sg.getStartRes() == 0 + && sg.getEndRes() == fixedRight + && sg.getEndRes() == av.alignment.getWidth()-1 + ) + { + sg.setEndRes(av.alignment.getWidth() + startres - lastres); + fixedRight = sg.getEndRes(); + } + + // Is it valid with fixed columns?? + // Find the next gap before the end + // of the visible region boundary + boolean blank = false; + for (fixedRight = fixedRight; + fixedRight > lastres; + fixedRight--) + { + blank = true; + + for (g = 0; g < groupSize; g++) + { + for (int j = 0; j < startres - lastres; j++) + { + if (!jalview.util.Comparison.isGap( + groupSeqs[g].getCharAt(fixedRight - j))) + { + blank = false; + break; } + } + } + if (blank) + break; + } - sg.setEndRes(sg.getEndRes() + (res - lastres)); + if (!blank) + { + 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 = alWidth+startres-lastres; + } + else + { + endEditing(); + return; + } + } + } - for (int s = 0; s < sg.getSize(); s++) - { - seq = sg.getSequenceAt(s); - - for (int j = res; j < lastres; j++) - { - if (seq.getSequence().length() <= j) - { - continue; - } - - if (!jalview.util.Comparison.isGap( - seq.getSequence().charAt(j))) - { - // Not a gap, block edit not valid - endEditing(); - return; - } - } - } - if(res res) - { - deleteChar(res, seq); - } - } - } + for (g = 0; g < groupSize; g++) + { + if (insertGap) + { + // dragging to the right + for (int j = lastres; j < startres; j++) + { + if (fixedColumns && fixedRight != -1) + { + insertChar(j, groupSeqs[g], fixedRight); } + else + insertChar(j, groupSeqs[g]); + } } - else /////Editing a single sequence/////////// + else { - seq = av.alignment.getSequenceAt(startseq); - if ((res < av.getAlignment().getWidth()) && (res > lastres)) + // dragging to the left + for (int j = lastres; j > startres; j--) + { + if (fixedColumns && fixedRight != -1) { - // dragging to the right - for (int j = lastres; j < res; j++) - { - insertChar(j, seq, j); - } + deleteChar(startres, groupSeqs[g], fixedRight); } - else if ((res < av.getAlignment().getWidth()) && - (res < lastres)) + else { - // dragging to the left - for (int j = lastres; j > res; j--) - { - if (jalview.util.Comparison.isGap( - av.alignment.getSequenceAt(startseq) - .getSequence().charAt(res))) - { - deleteChar(res, seq); - } - else - { - break; - } - } + deleteChar(startres, groupSeqs[g]); } + } } + } + } + else /////Editing a single sequence/////////// + { + if (insertGap) + { + // dragging to the right + for (int j = lastres; j < startres; j++) + { + if (fixedColumns && fixedRight != -1) + { + insertChar(j, seq, fixedRight); + } + else + insertChar(j, seq); + } + } + else + { + // dragging to the left + for (int j = lastres; j > startres; j--) + { + if (fixedColumns && fixedRight != -1) + { + deleteChar(startres, seq, fixedRight); + } + else + { + deleteChar(startres, seq); + } + } + } } - mouseDragging = true; - if(scrollThread!=null) - scrollThread.setEvent(evt); - - endEdit = res; - lastres = res; + lastres = startres; seqCanvas.repaint(); } + + /** + * 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) + { + //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--) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn))) + { + //Theres a space, so break and insert the gap + break; + } + } + + 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; + } + + seq.deleteCharAt(blankColumn); + seq.insertCharAt(j, av.getGapCharacter()); + seqEditOccurred = 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) + { + 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(); + } /** * DOCUMENT ME! * @@ -681,7 +1127,8 @@ public class SeqPanel extends JPanel implements MouseListener, public void mouseWheelMoved(MouseWheelEvent e) { - if (mouseWheelPressed) + e.consume(); + /* if (mouseWheelPressed) { Font font = av.getFont(); int fontSize = font.getSize(); @@ -690,10 +1137,13 @@ public class SeqPanel extends JPanel implements MouseListener, else if (fontSize > 1) fontSize--; + + av.setFont(new Font(font.getName(), font.getStyle(), fontSize)); + ap.fontChanged(); } - else + else*/ { if (e.getWheelRotation() > 0) ap.scrollUp(false); @@ -704,78 +1154,6 @@ public class SeqPanel extends JPanel implements MouseListener, } - /** - * DOCUMENT ME! - * - * @param j DOCUMENT ME! - * @param seq DOCUMENT ME! - */ - void insertChar(int j, SequenceI seq, int blankColumn) - { - if(av.hasHiddenColumns) - { - //Find the next gap before the end of the visible region boundary - int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j); - if(lastCol != j) - { - if (!groupEditing || lastCol <= j) - { - blankColumn = lastCol; - //If lastCol > j, theres a boundary after the gap insertion - if (lastCol > j) - { - for (blankColumn = lastCol; blankColumn > j; blankColumn--) - { - if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn))) - { - //Theres a space, so break and insert the gap - break; - } - } - - if (blankColumn <= j) - { - endEditing(); - return; - } - } - - } - - // Editing with hidden regions only!! - seq.deleteCharAt(blankColumn); - } - } - - seq.insertCharAt(j, av.getGapCharacter()); - seqEditOccurred = true; - } - - /** - * DOCUMENT ME! - * - * @param j DOCUMENT ME! - * @param seq DOCUMENT ME! - */ - public void deleteChar(int j, SequenceI seq) - { - if (av.hasHiddenColumns) - { - //Find the next gap before the end of the visible region boundary - int lastCol = av.getColumnSelection().getHiddenRegionBoundary(j); - - //If lastCol > j, theres a boundary after the gap insertion - if (lastCol > j) - { - seq.insertCharAt(lastCol, av.getGapCharacter()); - } - } - - seq.deleteCharAt(j); - seqEditOccurred = true; - - seqCanvas.repaint(); - } /** * DOCUMENT ME! @@ -784,12 +1162,14 @@ public class SeqPanel extends JPanel implements MouseListener, */ void editOccurred() { - if (endEdit == startEdit) + if (!seqEditOccurred) { ap.alignFrame.historyList.pop(); ap.alignFrame.updateEditMenuBar(); } + endEditing(); + av.firePropertyChange("alignment", null,av.getAlignment().getSequences()); } @@ -813,13 +1193,12 @@ 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) return; - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); if ((sequence == null) || (res > sequence.getLength())) @@ -843,7 +1222,7 @@ 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)) { @@ -859,57 +1238,84 @@ public class SeqPanel extends JPanel implements MouseListener, (allGroups[i].getEndRes() >= res)) { stretchGroup = allGroups[i]; - av.setSelectionGroup(stretchGroup); - break; } } } + + av.setSelectionGroup(stretchGroup); + } - if (stretchGroup == null) + + if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - // 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()) + Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); + Vector links = new Vector(); + for (int i = 0; i < allFeatures.size(); i++) { - SliderPanel.setConservationSlider(ap, - av.getGlobalColourScheme(), "Background"); + 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)); + } + } } - 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); + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links); pop.show(this, evt.getX(), evt.getY()); + return; + } - // edit the properties of existing group + if (av.cursorMode) + { + seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorY = findSeq(evt); + seqCanvas.repaint(); + return; } - if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) + if (stretchGroup == null) { + //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.getGlobalColourScheme(), + "Background"); + } + + 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(); } @@ -930,8 +1336,8 @@ 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()); } @@ -950,7 +1356,8 @@ public class SeqPanel extends JPanel implements MouseListener, changeEndRes = false; changeStartRes = false; stretchGroup = null; - PaintRefresher.Refresh(av.alignment); + + PaintRefresher.Refresh(this, av.getSequenceSetId()); } /** @@ -971,10 +1378,9 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - - if(y > av.alignment.getHeight()) + if(res> av.alignment.getWidth()) { - y = av.alignment.getHeight() -1; + res = av.alignment.getWidth()-1; } if (stretchGroup.getEndRes() == res) @@ -1033,7 +1439,7 @@ 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); } @@ -1061,6 +1467,27 @@ public class SeqPanel extends JPanel implements MouseListener, seqCanvas.repaint(); } + void scrollCanvas(MouseEvent evt) + { + if(evt==null) + { + if(scrollThread!=null) + { + scrollThread.running = false; + scrollThread = null; + } + mouseDragging = false; + } + else + { + if (scrollThread == null) + scrollThread = new ScrollThread(); + + mouseDragging = true; + scrollThread.setEvent(evt); + } + + } // this class allows scrolling off the bottom of the visible alignment @@ -1106,11 +1533,11 @@ public class SeqPanel extends JPanel implements MouseListener, if (mouseDragging && (evt.getX() < 0)) { - running = ap.scrollRight(true); + running = ap.scrollRight(false); } else if (mouseDragging && (evt.getX() >= getWidth())) { - running = ap.scrollRight(false); + running = ap.scrollRight(true); } }