X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=f4f2cfd2bebf7e3aef5ed8ed85b38ed687497335;hb=cbd8cafe5f1d302cf490d34a96f8231659afd402;hp=5ecc613e009f7d640ad4fa985a1e7ca22ad19f54;hpb=c95df1d1e8746c6fa31b94c2bf8505f25a30c168;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 5ecc613..f4f2cfd 100755 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 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 @@ -19,16 +19,19 @@ package jalview.appletgui; +import java.util.*; + import java.awt.*; import java.awt.event.*; +import jalview.commands.*; import jalview.datamodel.*; import jalview.schemes.*; - -import java.util.Vector; +import jalview.structure.SequenceListener; +import jalview.structure.StructureSelectionManager; public class SeqPanel - extends Panel implements MouseMotionListener, MouseListener + extends Panel implements MouseMotionListener, MouseListener, SequenceListener { public SeqCanvas seqCanvas; @@ -60,6 +63,11 @@ public class SeqPanel boolean mouseWheelPressed = false; Point lastMousePress; + EditCommand editCommand; + + StructureSelectionManager ssm; + + public SeqPanel(AlignViewport avp, AlignmentPanel p) { this.av = avp; @@ -72,408 +80,482 @@ public class SeqPanel seqCanvas.addMouseMotionListener(this); seqCanvas.addMouseListener(this); + ssm = StructureSelectionManager.getStructureSelectionManager(); + ssm.addStructureViewerListener(this); seqCanvas.repaint(); } 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; - } - - 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); - } - 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).removeAllElements(); - 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()); - } - - 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()); - - } - public void mousePressed(MouseEvent evt) - { - lastMousePress = evt.getPoint(); - - //For now, ignore the mouseWheel font resizing on Macs - //As the Button2_mask always seems to be true - if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) == - InputEvent.BUTTON2_MASK && !av.MAC) - { - mouseWheelPressed = true; - return; - } - - if (evt.isShiftDown() - || evt.isControlDown() - || evt.isAltDown()) - { - if (evt.isControlDown() || evt.isAltDown()) - { - groupEditing = true; - } - editingSeqs = true; - } - else - { - doMousePressedDefineMode(evt); - 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())) - { - startseq = seq; - lastres = res; - } - else - { - startseq = -1; - lastres = -1; - } + editCommand = null; + } - return; - } + void setCursorRow() + { + seqCanvas.cursorY = getKeyboardNo1() - 1; + scrollToVisible(); + } + + void setCursorColumn() + { + seqCanvas.cursorX = getKeyboardNo1() - 1; + scrollToVisible(); + } + + void setCursorRowAndColumn() + { + if (keyboardNo2 == null) + { + keyboardNo2 = new StringBuffer(); + } + else + { + seqCanvas.cursorX = getKeyboardNo1() - 1; + seqCanvas.cursorY = getKeyboardNo2() - 1; + scrollToVisible(); + } + } + + void setCursorPosition() + { + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + + seqCanvas.cursorX = sequence.findIndex( + getKeyboardNo1() - 1 + ); + scrollToVisible(); + } + + void moveCursor(int dx, int dy) + { + seqCanvas.cursorX += dx; + seqCanvas.cursorY += dy; + 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.cursorX < maxWidth + && seqCanvas.cursorX > 0) + { + seqCanvas.cursorX += dx; + } + + if (seqCanvas.cursorX >= maxWidth + || !av.colSel.isVisible(seqCanvas.cursorX)) + { + seqCanvas.cursorX = original; + } + } + 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); + } + while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes)) + { + + if (!ap.scrollRight(false)) + { + break; + } + } + while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(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 < sg.getSize(); i++) + { + int index = av.alignment.findIndex(sg.getSequenceAt(i)); + if (index > max) + { + max = index; + } + if (index < min) + { + min = index; + } + } + + max++; + + if (topLeft) + { + sg.setStartRes(seqCanvas.cursorX); + if (sg.getEndRes() < seqCanvas.cursorX) + { + sg.setEndRes(seqCanvas.cursorX); + } + + min = seqCanvas.cursorY; + } + else + { + sg.setEndRes(seqCanvas.cursorX); + if (sg.getStartRes() > seqCanvas.cursorX) + { + sg.setStartRes(seqCanvas.cursorX); + } + + max = seqCanvas.cursorY + 1; + } + + if (min > max) + { + // Only the user can do this + av.setSelectionGroup(null); + } + else + { + // Now add any sequences between min and max + sg.getSequences(null).removeAllElements(); + 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.paintAlignment(false); + } + + void insertGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(true, seqCanvas.cursorX + getKeyboardNo1()); + endEditing(); + } + + void deleteGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX + getKeyboardNo1(); + editSequence(false, seqCanvas.cursorX); + endEditing(); + } + + void numberPressed(char value) + { + if (keyboardNo1 == null) + { + keyboardNo1 = new StringBuffer(); + } + + if (keyboardNo2 != null) + { + keyboardNo2.append(value); + } + else + { + keyboardNo1.append(value); + } + } + + int getKeyboardNo1() + { + if (keyboardNo1 == null) + return 1; + else + { + int value = Integer.parseInt(keyboardNo1.toString()); + keyboardNo1 = null; + return value; + } + } + + int getKeyboardNo2() + { + if (keyboardNo2 == null) + return 1; + else + { + int value = Integer.parseInt(keyboardNo2.toString()); + keyboardNo2 = null; + return value; + } + } + + + 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()); + + } + + public void mousePressed(MouseEvent evt) + { + lastMousePress = evt.getPoint(); + + //For now, ignore the mouseWheel font resizing on Macs + //As the Button2_mask always seems to be true + if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) == + InputEvent.BUTTON2_MASK && !av.MAC) + { + mouseWheelPressed = true; + return; + } + + if (evt.isShiftDown() + || evt.isControlDown() + || evt.isAltDown()) + { + if (evt.isControlDown() || evt.isAltDown()) + { + groupEditing = true; + } + editingSeqs = true; + } + else + { + doMousePressedDefineMode(evt); + return; + } - public void mouseClicked(MouseEvent evt){} + int seq = findSeq(evt); + int res = findRes(evt); + + if (seq < 0 || res < 0) + { + return; + } + + if ( (seq < av.getAlignment().getHeight()) && + (res < av.getAlignment().getSequenceAt(seq).getLength())) + { + startseq = seq; + lastres = res; + } + else + { + startseq = -1; + lastres = -1; + } + + return; + } + public void mouseClicked(MouseEvent evt) + {} public void mouseReleased(MouseEvent evt) { mouseDragging = false; mouseWheelPressed = false; + ap.paintAlignment(true); if (!editingSeqs) { - doMouseReleasedDefineMode(evt); - return; + doMouseReleasedDefineMode(evt); + return; } - editOccurred(); + endEditing(); - endEditing(); - ap.repaint(); } - int startWrapBlock=-1; - int wrappedBlock=-1; + int startWrapBlock = -1; + int wrappedBlock = -1; int findRes(MouseEvent evt) - { - int res = 0; - int x = evt.getX(); - - if (av.wrapAlignment) { + int res = 0; + int x = evt.getX(); - int hgap = av.charHeight; - if (av.scaleAboveWrapped) - hgap += av.charHeight; + if (av.wrapAlignment) + { - int cHeight = av.getAlignment().getHeight() * av.charHeight - + hgap + seqCanvas.getAnnotationHeight(); + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + { + hgap += av.charHeight; + } + + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); y -= hgap; x -= seqCanvas.LABEL_WEST; - int cwidth = seqCanvas.getWrappedCanvasWidth(getSize().width); - if(cwidth<1) + if (cwidth < 1) + { return 0; + } wrappedBlock = y / cHeight; wrappedBlock += av.getStartRes() / cwidth; res = wrappedBlock * cwidth + x / av.getCharWidth(); - } - else - { + } + else + { res = (x / av.getCharWidth()) + av.getStartRes(); - } - - if(av.hasHiddenColumns) - res = av.getColumnSelection().adjustForHiddenColumns(res); + } - return res; + if (av.hasHiddenColumns) + { + res = av.getColumnSelection().adjustForHiddenColumns(res); + } - } + return res; - int findSeq(MouseEvent evt) - { + } - int seq = 0; - int y = evt.getY(); + int findSeq(MouseEvent evt) + { - if (av.wrapAlignment) - { - int hgap = av.charHeight; - if (av.scaleAboveWrapped) - hgap += av.charHeight; + int seq = 0; + int y = evt.getY(); - int cHeight = av.getAlignment().getHeight() * av.charHeight - + hgap + seqCanvas.getAnnotationHeight(); + if (av.wrapAlignment) + { + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + { + hgap += av.charHeight; + } - y -= hgap; + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); - seq = Math.min( (y % cHeight) / av.getCharHeight(), - av.alignment.getHeight() -1); - if(seq<0) - seq = 0; - } - else - { - seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(), - av.alignment.getHeight() -1); - if(seq<0) - seq = 0; - } + y -= hgap; - return seq; - } + seq = Math.min( (y % cHeight) / av.getCharHeight(), + av.alignment.getHeight() - 1); + if (seq < 0) + { + seq = 0; + } + } + else + { + seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(), + av.alignment.getHeight() - 1); + if (seq < 0) + { + seq = 0; + } + } + return seq; + } public void doMousePressed(MouseEvent evt) { - ap.alignFrame.addHistoryItem(new HistoryItem( - "Edit Sequence", av.alignment, HistoryItem.EDIT)); int seq = findSeq(evt); int res = findRes(evt); @@ -497,38 +579,83 @@ public class SeqPanel return; } + + String lastMessage; + public void mouseOverSequence(SequenceI sequence, int index) + { + String tmp = sequence.hashCode()+index+""; + if (lastMessage == null || !lastMessage.equals(tmp)) + ssm.mouseOverSequence(sequence, index); + + lastMessage = tmp; + } + + + public void highlightSequence(jalview.datamodel.SequenceI seq, int index) + { + if(av.alignment.findIndex(seq)>-1) + { + SearchResults highlight = new SearchResults(); + highlight.addResult(seq,index,index); + seqCanvas.highlightSearchResults(highlight); + } + } + + public void updateColours(SequenceI seq, int index) + { + System.out.println("update the seqPanel colours"); + //repaint(); + } + public void mouseMoved(MouseEvent evt) { int res = findRes(evt); int seq = findSeq(evt); - if (seq >= av.getAlignment().getHeight() || seq<0 || res<0) + if (seq >= av.getAlignment().getHeight() || seq < 0 || res < 0) { + if (tooltip != null) + { + tooltip.setTip(""); + } return; } SequenceI sequence = av.getAlignment().getSequenceAt(seq); if (res > sequence.getLength()) { + if (tooltip != null) + { + tooltip.setTip(""); + } return; } + + if (ssm != null) + mouseOverSequence(sequence, sequence.findPosition(res)); + + StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + - sequence.getName()); + sequence.getName()); Object obj = null; if (av.alignment.isNucleotide()) { obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + - ""); - if(obj!=null) + ""); + if (obj != null) + { text.append(" Nucleotide: "); + } } else { obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); - if(obj!=null) + if (obj != null) + { text.append(" Residue: "); + } } if (obj != null) @@ -539,51 +666,72 @@ public class SeqPanel } } - if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) - { - seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); - } - ap.alignFrame.statusBar.setText(text.toString()); + StringBuffer tooltipText = new StringBuffer(); + SequenceGroup[] groups = av.alignment.findAllGroups(sequence); + if (groups != null) + { + for (int g = 0; g < groups.length; g++) + { + if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= 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()); + } + tooltipText.append("\n"); + } + } + } // use aa to see if the mouse pointer is on a if (av.showSequenceFeatures - && sequence.getSequenceFeatures()!=null - && av.featuresDisplayed!=null) + && sequence.getSequenceFeatures() != null + && av.featuresDisplayed != null) { - StringBuffer featureText = new StringBuffer(); - Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res)); + + Vector allFeatures = getAllFeaturesAtRes(sequence, + sequence.findPosition(res)); int index = 0; while (index < allFeatures.size()) { SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index); - featureText.append(sf.getType()+" "+sf.begin+":"+sf.end); + tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end); if (sf.getDescription() != null) - featureText.append(" " + sf.getDescription()); + { + tooltipText.append(" " + sf.getDescription()); + } - if (sf.getValue("status") != null ) + if (sf.getValue("status") != null) { String status = sf.getValue("status").toString(); - if(status.length()>0) - featureText.append(" (" + sf.getValue("status") + ")"); + if (status.length() > 0) + { + tooltipText.append(" (" + sf.getValue("status") + ")"); + } } - featureText.append("\n"); + tooltipText.append("\n"); index++; } + } - - if (tooltip == null) - tooltip = new Tooltip(featureText.toString(), seqCanvas); - else - tooltip.setTip(featureText.toString()); - - tooltip.repaint(); - + if (tooltip == null) + { + tooltip = new Tooltip(tooltipText.toString(), seqCanvas); + } + else + { + tooltip.setTip(tooltipText.toString()); } } @@ -591,7 +739,7 @@ public class SeqPanel { Vector allFeatures = new Vector(); int index = 0; - if(seq.getSequenceFeatures()!=null) + if (seq.getSequenceFeatures() != null) { while (index < seq.getSequenceFeatures().length) { @@ -633,9 +781,10 @@ public class SeqPanel fontSize++; } - - if(fontSize<1) + if (fontSize < 1) + { fontSize = 1; + } av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); av.charWidth = oldWidth; @@ -651,7 +800,7 @@ public class SeqPanel av.charWidth++; } - if(av.charWidth<1) + if (av.charWidth < 1) { av.charWidth = 1; } @@ -664,40 +813,44 @@ public class SeqPanel lastMousePress = evt.getPoint(); - ap.repaint(); + ap.paintAlignment(false); ap.annotationPanel.image = null; return; - } + } - if (!editingSeqs) - { - doMouseDraggedDefineMode(evt); - return; - } + if (!editingSeqs) + { + doMouseDraggedDefineMode(evt); + return; + } - int res = findRes(evt); + int res = findRes(evt); - if (res < 0) - { + if (res < 0) + { res = 0; - } + } - if ((lastres == -1) || (lastres == res)) - { + if ( (lastres == -1) || (lastres == res)) + { return; - } + } - if ( (res < av.getAlignment().getWidth()) && (res < lastres)) - { - // dragLeft, delete gap - editSequence(false, res); - } - else - editSequence(true, res); + if ( (res < av.getAlignment().getWidth()) && (res < lastres)) + { + // dragLeft, delete gap + editSequence(false, res); + } + else + { + editSequence(true, res); + } - mouseDragging = true; - if(scrollThread!=null) - scrollThread.setEvent(evt); + mouseDragging = true; + if (scrollThread != null) + { + scrollThread.setEvent(evt); + } } @@ -708,302 +861,357 @@ public class SeqPanel boolean fixedColumns = false; SequenceGroup sg = av.getSelectionGroup(); + SequenceI seq = av.alignment.getSequenceAt(startseq); - if (!groupEditing && av.hasHiddenRows) + if (!groupEditing && av.hasHiddenRows) + { + if (av.hiddenRepSequences != null + && av.hiddenRepSequences.containsKey(seq)) { - if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null) - { - groupEditing = true; - } + sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + groupEditing = true; } + } - //No group, but the sequence may represent a group - if (groupEditing - && sg == null - && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null) + StringBuffer message = new StringBuffer(); + if (groupEditing) + { + message.append("Edit group:"); + if (editCommand == null) { - groupEditing = false; + editCommand = new EditCommand("Edit Group"); } + } + else + { + message.append("Edit sequence: " + seq.getName()); + String label = seq.getName(); + if (label.length() > 10) + { + label = label.substring(0, 10); + } + if (editCommand == null) + { + editCommand = new EditCommand("Edit " + label); + } + } - SequenceI seq = av.alignment.getSequenceAt(startseq); - StringBuffer message = new StringBuffer(); - if (groupEditing) - message.append("Edit group:"); - else - message.append("Edit sequence: "+seq.getName()); - - if(insertGap) - message.append(" insert "); - else - message.append(" delete "); + if (insertGap) + { + message.append(" insert "); + } + else + { + message.append(" delete "); + } - message.append(Math.abs(startres-lastres)+" gaps."); - ap.alignFrame.statusBar.setText(message.toString()); + message.append(Math.abs(startres - lastres) + " gaps."); + ap.alignFrame.statusBar.setText(message.toString()); + //Are we editing within a selection group? + if (groupEditing + || (sg != null && sg.getSequences(av.hiddenRepSequences).contains(seq))) + { + fixedColumns = true; - //Are we editing within a selection group? - if (groupEditing - || (sg != null && sg.getSequences(true).contains(seq))) + //sg might be null as the user may only see 1 sequence, + //but the sequence represents a group + if (sg == null) { - fixedColumns = true; - - //sg might be null as the user may only see 1 sequence, - //but the sequence represents a group - if (sg == null) - { - sg = new SequenceGroup(null, null, false, false, false, 0, - av.alignment.getWidth()-1); - sg.addSequence(av.alignment.getSequenceAt(startseq), false); - } - - fixedLeft = sg.getStartRes(); - fixedRight = sg.getEndRes(); - - if ( (startres < fixedLeft && lastres >= fixedLeft) - || (startres >= fixedLeft && lastres < fixedLeft) - || (startres > fixedRight && lastres <=fixedRight) - || (startres <= fixedRight && lastres > fixedRight)) + if (av.hiddenRepSequences == null + || !av.hiddenRepSequences.containsKey(seq)) { endEditing(); return; } - if (fixedLeft > startres) + sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + } + + fixedLeft = sg.getStartRes(); + fixedRight = sg.getEndRes(); + + if ( (startres < fixedLeft && lastres >= fixedLeft) + || (startres >= fixedLeft && lastres < fixedLeft) + || (startres > fixedRight && lastres <= fixedRight) + || (startres <= fixedRight && lastres > fixedRight)) + { + endEditing(); + return; + } + + if (fixedLeft > startres) + { + fixedRight = fixedLeft - 1; + fixedLeft = 0; + } + else if (fixedRight < startres) + { + fixedLeft = fixedRight; + fixedRight = -1; + } + } + + if (av.hasHiddenColumns) + { + fixedColumns = true; + int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); + int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + + if ( (insertGap && startres > y1 && lastres < y1) + || (!insertGap && startres < y2 && lastres > y2)) + { + endEditing(); + return; + } + + //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); + //Selection spans a hidden region + if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1)) + { + if (startres >= y2) { - fixedRight = fixedLeft - 1; - fixedLeft = 0; + fixedLeft = y2; } - else if (fixedRight < startres) + else { - fixedLeft = fixedRight; - fixedRight = -1; + fixedRight = y2 - 1; } } + } - - if(av.hasHiddenColumns ) + 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++) { - 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; - } - - //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; - } - } + groupSeqs[g] = (SequenceI) vseqs.elementAt(g); } - - if (groupEditing) + // drag to right + if (insertGap) { - // 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 + ) { - //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(); - } + 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--) + // 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++) { - blank = true; - for (int s = 0; s < sg.getSize(true); s++) + for (int j = 0; j < startres - lastres; j++) { - seq = (SequenceI)sg.getSequences(true).elementAt(s); - for (int j = 0; j < startres - lastres; j++) + if (!jalview.util.Comparison.isGap( + groupSeqs[g].getCharAt(fixedRight - j))) { - if (!jalview.util.Comparison.isGap( - seq.getCharAt(fixedRight - j))) - { - blank = false; - break; - } + blank = false; + break; } } - if (blank) - break; } + if (blank) + { + break; + } + } - if (!blank) + if (!blank) + { + if (sg.getSize() == av.alignment.getHeight()) { - if(sg.getSize(false) == av.alignment.getHeight() ) + if ( (av.hasHiddenColumns + && + startres < av.getColumnSelection().getHiddenBoundaryRight(startres))) { - if((av.hasHiddenColumns - && startres alWidth) { - int hwidth = av.alignment.getHiddenSequences().getWidth(); - if(hwidth>alWidth) - alWidth = hwidth; + 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; } + //We can still insert gaps if the selectionGroup + //contains all the sequences + sg.setEndRes(sg.getEndRes() + startres - lastres); + fixedRight = alWidth + startres - lastres; + } + else + { + endEditing(); + return; } } + } + // drag to left + else if (!insertGap) + { + /// Are we able to delete? + // ie are all columns blank? - // drag to left - else if(!insertGap) + for (g = 0; g < groupSize; g++) { - /// Are we able to delete? - // ie are all columns blank? - - for (int s = 0; s < sg.getSize(true); s++) + for (int j = startres; j < lastres; j++) { - seq = (SequenceI)sg.getSequences(true).elementAt(s); - - for (int j = startres; j < lastres; j++) + if (groupSeqs[g].getLength() <= j) { - if (seq.getSequence().length() <= j) - { - continue; - } + continue; + } - if (!jalview.util.Comparison.isGap( - seq.getSequence().charAt(j))) - { - // Not a gap, block edit not valid - endEditing(); - return; - } + if (!jalview.util.Comparison.isGap( + groupSeqs[g].getCharAt(j))) + { + // Not a gap, block edit not valid + endEditing(); + return; } } } + } - - for (int i = 0; i < sg.getSize(true); i++) + if (insertGap) + { + // dragging to the right + if (fixedColumns && fixedRight != -1) { - seq = (SequenceI) sg.getSequences(true).elementAt(i); - - if (insertGap) + for (int j = lastres; j < startres; j++) { - // dragging to the right - for (int j = lastres; j < startres; j++) - { - if (fixedColumns && fixedRight != -1) - { - insertChar(j, seq, fixedRight); - } - else - insertChar(j, seq); - } + insertChar(j, groupSeqs, fixedRight); } - else + } + else + { + editCommand.appendEdit(EditCommand.INSERT_GAP, + groupSeqs, + startres, startres - lastres, + av.alignment, + true); + } + } + else + { + // dragging to the left + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j > startres; j--) { - // dragging to the left - for (int j = lastres; j > startres; j--) - { - if (fixedColumns && fixedRight != -1) - { - deleteChar(startres, seq, fixedRight); - } - else - { - 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/////////// + } + else /////Editing a single sequence/////////// + { + if (insertGap) { - if (insertGap) + // dragging to the right + if (fixedColumns && fixedRight != -1) { - // dragging to the right for (int j = lastres; j < startres; j++) { - if (fixedColumns && fixedRight != -1) - { - insertChar(j, seq, fixedRight); - } - else - insertChar(j, seq); + insertChar(j, new SequenceI[] + {seq}, fixedRight); } } else { - // dragging to the left + editCommand.appendEdit(EditCommand.INSERT_GAP, + new SequenceI[] + {seq}, + lastres, startres - lastres, + av.alignment, + true); + } + } + else + { + // dragging to the left + if (fixedColumns && fixedRight != -1) + { for (int j = lastres; j > startres; j--) { - if (fixedColumns && fixedRight != -1) + if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) { - deleteChar(startres, seq, fixedRight); + endEditing(); + break; } - else + deleteChar(startres, new SequenceI[] + {seq}, fixedRight); + } + } + else + { + //could be a keyboard edit trying to delete none gaps + int max = 0; + for (int m = startres; m < lastres; m++) + { + if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) { - deleteChar(startres, seq); + break; } + max++; + } + + if (max > 0) + { + editCommand.appendEdit(EditCommand.DELETE_GAP, + new SequenceI[] + {seq}, + startres, max, + av.alignment, + true); } } } + } - lastres = startres; - seqCanvas.repaint(); + 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) + void insertChar(int j, SequenceI[] seq, int fixedColumn) + { + int blankColumn = fixedColumn; + for (int s = 0; s < seq.length; s++) { //Find the next gap before the end of the visible region boundary //If lastCol > j, theres a boundary after the gap insertion - int blankColumn = fixedColumn; + for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) { - if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn))) + if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn))) { //Theres a space, so break and insert the gap break; @@ -1012,81 +1220,40 @@ public class SeqPanel 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; - } + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + blankColumn, 1, av.alignment, true); - seq.deleteCharAt(j); - seqEditOccurred = true; - seqCanvas.repaint(); - } + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + j, 1, av.alignment, + true); - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - */ - void editOccurred() - { - if (!seqEditOccurred) - { - ap.alignFrame.historyList.pop(); - ap.alignFrame.updateEditMenuBar(); - } + } - endEditing(); + void deleteChar(int j, SequenceI[] seq, int fixedColumn) + { - av.firePropertyChange("alignment", null,av.getAlignment().getSequences()); + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + j, 1, av.alignment, true); - } + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + fixedColumn, 1, av.alignment, true); + } ////////////////////////////////////////// /////Everything below this is for defining the boundary of the rubberband ////////////////////////////////////////// public void doMousePressedDefineMode(MouseEvent evt) { - - if (scrollThread != null) { scrollThread.running = false; @@ -1096,10 +1263,12 @@ public class SeqPanel int res = findRes(evt); int seq = findSeq(evt); oldSeq = seq; - startWrapBlock=wrappedBlock; + startWrapBlock = wrappedBlock; - if(seq==-1) + if (seq == -1) + { return; + } SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); @@ -1124,7 +1293,7 @@ public class SeqPanel } } - else if (!stretchGroup.getSequences(false).contains(sequence) + else if (!stretchGroup.getSequences(null).contains(sequence) || stretchGroup.getStartRes() > res || stretchGroup.getEndRes() < res) { @@ -1147,16 +1316,15 @@ public class SeqPanel av.setSelectionGroup(stretchGroup); } - // DETECT RIGHT MOUSE BUTTON IN AWT if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) == - InputEvent.BUTTON3_MASK) + InputEvent.BUTTON3_MASK) { Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res)); Vector links = null; - if(allFeatures!=null) + if (allFeatures != null) { for (int i = 0; i < allFeatures.size(); i++) { @@ -1174,7 +1342,6 @@ public class SeqPanel APopupMenu popup = new APopupMenu(ap, null, links); this.add(popup); popup.show(this, evt.getX(), evt.getY()); - ap.repaint(); return; } @@ -1186,48 +1353,56 @@ public class SeqPanel return; } - //Only if left mouse button do we want to change group sizes + //Only if left mouse button do we want to change group sizes - if (stretchGroup == null) + 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()) { - // 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"); - } - + SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), + "Background"); + } + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), + "Background"); } + + } } public void doMouseReleasedDefineMode(MouseEvent evt) { if (stretchGroup == null) { - return; + return; } - if(stretchGroup.cs!=null) + if (stretchGroup.cs != null) { if (stretchGroup.cs instanceof ClustalxColourScheme) { ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX( - stretchGroup.getSequences(true), + 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, @@ -1243,8 +1418,8 @@ public class SeqPanel changeEndRes = false; changeStartRes = false; stretchGroup = null; - PaintRefresher.Refresh(av.alignment); - ap.repaint(); + PaintRefresher.Refresh(ap, av.getSequenceSetId()); + ap.paintAlignment(true); } public void doMouseDraggedDefineMode(MouseEvent evt) @@ -1252,125 +1427,132 @@ public class SeqPanel int res = findRes(evt); int y = findSeq(evt); - if(wrappedBlock!=startWrapBlock) + if (wrappedBlock != startWrapBlock) + { return; + } - if (stretchGroup == null) - { - return; - } + if (stretchGroup == null) + { + return; + } + + mouseDragging = true; - mouseDragging = true; + if (y > av.alignment.getHeight()) + { + y = av.alignment.getHeight() - 1; + } + if (res >= av.alignment.getWidth()) + { + res = av.alignment.getWidth() - 1; + } - if(y > av.alignment.getHeight()) - { - y = av.alignment.getHeight() -1; - } + if (stretchGroup.getEndRes() == res) + { + // Edit end res position of selected group + changeEndRes = true; + } + else if (stretchGroup.getStartRes() == res) + { + // Edit start res position of selected group + changeStartRes = true; + } - if(res>av.alignment.getWidth()) - res = av.alignment.getWidth()-1; + if (res < 0) + { + res = 0; + } - if (stretchGroup.getEndRes() == res) + if (changeEndRes) + { + if (res > (stretchGroup.getStartRes() - 1)) { - // Edit end res position of selected group - changeEndRes = true; + stretchGroup.setEndRes(res); } - else if (stretchGroup.getStartRes() == res) + } + else if (changeStartRes) + { + if (res < (stretchGroup.getEndRes() + 1)) { - // Edit start res position of selected group - changeStartRes = true; + stretchGroup.setStartRes(res); } + } - if (res < 0) - { - res = 0; - } + int dragDirection = 0; - if (changeEndRes) - { - if (res > (stretchGroup.getStartRes() - 1)) - { - stretchGroup.setEndRes(res); - } - } - else if (changeStartRes) - { - if (res < (stretchGroup.getEndRes() + 1)) - { - stretchGroup.setStartRes(res); - } - } + if (y > oldSeq) + { + dragDirection = 1; + } + else if (y < oldSeq) + { + dragDirection = -1; + } + + while ( (y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) + { + // This routine ensures we don't skip any sequences, as the + // selection is quite slow. + Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - int dragDirection = 0; + oldSeq += dragDirection; - if (y > oldSeq) - { - dragDirection = 1; - } - else if (y < oldSeq) + if (oldSeq < 0) { - dragDirection = -1; + break; } + Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) + if (stretchGroup.getSequences(null).contains(nextSeq)) { - // This routine ensures we don't skip any sequences, as the - // selection is quite slow. - Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - - oldSeq += dragDirection; - - if(oldSeq<0) - break; - - Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - - if (stretchGroup.getSequences(false).contains(nextSeq)) - { - stretchGroup.deleteSequence(seq, false); - } - else - { - if (seq != null) - { - stretchGroup.addSequence(seq, false); - } + stretchGroup.deleteSequence(seq, false); + } + else + { + if (seq != null) + { + stretchGroup.addSequence(seq, false); + } - stretchGroup.addSequence(nextSeq, false); - } + stretchGroup.addSequence(nextSeq, false); } + } - if(oldSeq < 0) - oldSeq = -1; + if (oldSeq < 0) + { + oldSeq = -1; + } + if (res > av.endRes || res < av.startRes + || y < av.startSeq || y > av.endSeq) + { + mouseExited(evt); + } - if(res>av.endRes || resav.endSeq) - { - mouseExited(evt); - } + if (scrollThread != null) + { + scrollThread.setEvent(evt); + } - if (scrollThread != null) - { - scrollThread.setEvent(evt); - } + seqCanvas.repaint(); + } - seqCanvas.repaint(); + public void mouseEntered(MouseEvent e) + { + if (oldSeq < 0) + { + oldSeq = 0; } - public void mouseEntered(MouseEvent e) + if (scrollThread != null) { - if (oldSeq < 0) - oldSeq = 0; - - if (scrollThread != null) - { - scrollThread.running = false; - scrollThread = null; - } + scrollThread.running = false; + scrollThread = null; } + } public void mouseExited(MouseEvent e) { @@ -1379,7 +1561,7 @@ public class SeqPanel return; } - if (mouseDragging && scrollThread==null) + if (mouseDragging && scrollThread == null) { scrollThread = new ScrollThread(); } @@ -1387,9 +1569,9 @@ public class SeqPanel void scrollCanvas(MouseEvent evt) { - if(evt==null) + if (evt == null) { - if(scrollThread!=null) + if (scrollThread != null) { scrollThread.running = false; scrollThread = null; @@ -1399,13 +1581,15 @@ public class SeqPanel else { if (scrollThread == null) + { scrollThread = new ScrollThread(); + } mouseDragging = true; scrollThread.setEvent(evt); } - } + } // this class allows scrolling off the bottom of the visible alignment class ScrollThread