X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=a20165a78123a2ffbe1ba0d85225a08d37e50f95;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=536d178c160e19f685ddfcc61815c3c191a7d98d;hpb=1ab3860add27db695e8471783bf775ecff1fdae9;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 536d178..a20165a 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) 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 @@ -18,15 +18,15 @@ */ package jalview.gui; -import jalview.datamodel.*; - -import jalview.schemes.*; +import java.util.*; import java.awt.*; import java.awt.event.*; - import javax.swing.*; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.schemes.*; /** * DOCUMENT ME! @@ -34,207 +34,318 @@ import javax.swing.*; * @author $author$ * @version $Revision$ */ -public class SeqPanel extends JPanel implements MouseListener, +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; - - 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) - { - 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); - } + /** 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()) + { + 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) { 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 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(); - int cHeight = av.getAlignment().getHeight() * av.charHeight - + hgap + seqCanvas.getAnnotationHeight(); + y -= hgap; - y -= hgap; + seq = Math.min( (y % cHeight) / av.getCharHeight(), + av.alignment.getHeight() - 1); + } + else + { + seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(), + av.alignment.getHeight() - 1); + } - seq = ( (y % cHeight) / av.getCharHeight()); - } - else - { - seq = (y / av.getCharHeight()) + av.getStartSeq(); - } + return seq; + } - return seq; - } + 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; + } - void endEditing() - { - startseq = -1; - lastres = -1; - seqEditOccurred = false; - editingSeqs = false; - groupEditing = false; - keyboardNo1 = null; - keyboardNo2 = null; + if ( (features[i].getBegin() <= res) && + (features[i].getEnd() >= res)) + { + tmp.addElement(features[i]); + } + } } - void setCursorRow() + features = new SequenceFeature[tmp.size()]; + for (int i = 0; i < tmp.size(); i++) { - seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1; - scrollToVisible(); + features[i] = (SequenceFeature) tmp.elementAt(i); } - void setCursorColumn() + return features; + } + + Vector getAllFeaturesAtRes(SequenceI seq, int res) + { + Vector allFeatures = new Vector(); + int index = 0; + if (seq.getSequenceFeatures() != null && av.featuresDisplayed != null) { - seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1; - scrollToVisible(); + 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() + { + if (editCommand != null && editCommand.getSize() > 0) + { + ap.alignFrame.addHistoryItem(editCommand); + av.firePropertyChange("alignment", null, + av.getAlignment().getSequences()); } - void setCursorRowAndColumn() + startseq = -1; + lastres = -1; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + editCommand = 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; + if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX)) { - if(keyboardNo2==null) + int original = seqCanvas.cursorX - dx; + int maxWidth = av.alignment.getWidth(); + + while (!av.colSel.isVisible(seqCanvas.cursorX) + && seqCanvas.cursorX < maxWidth + && seqCanvas.cursorX > 0) { - keyboardNo2 = new StringBuffer(); + seqCanvas.cursorX += dx; } - else + + if (seqCanvas.cursorX >= maxWidth + || !av.colSel.isVisible(seqCanvas.cursorX)) { - seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; - seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1; - scrollToVisible(); + seqCanvas.cursorX = original; } } - void setCursorPosition() - { - SequenceI sequence = - (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + scrollToVisible(); + } - seqCanvas.cursorX = sequence.findIndex( - getKeyboardNo(keyboardNo1)-1 - ); - scrollToVisible(); + void scrollToVisible() + { + if (seqCanvas.cursorX < 0) + { + seqCanvas.cursorX = 0; } - - void moveCursor(int dx, int dy) + else if (seqCanvas.cursorX > av.alignment.getWidth() - 1) { - seqCanvas.cursorX += dx; - seqCanvas.cursorY += dy; - scrollToVisible(); + seqCanvas.cursorX = av.alignment.getWidth() - 1; } - void scrollToVisible() + if (seqCanvas.cursorY < 0) { - 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; - + seqCanvas.cursorY = 0; + } + else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) + { + seqCanvas.cursorY = av.alignment.getHeight() - 1; + } - endEditing(); + endEditing(); + if (av.wrapAlignment) + { + ap.scrollToWrappedVisible(seqCanvas.cursorX); + } + else + { while (seqCanvas.cursorY < av.startSeq) { ap.scrollUp(true); @@ -243,685 +354,894 @@ public class SeqPanel extends JPanel implements MouseListener, { ap.scrollUp(false); } - while (seqCanvas.cursorX < av.startRes) - { - if(!ap.scrollRight(false)) - break; - } - while (seqCanvas.cursorX > av.endRes) + if (!av.wrapAlignment) { - if(!ap.scrollRight(true)) - break; + 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); - setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), - seqCanvas.cursorX, seqCanvas.cursorY); + seqCanvas.repaint(); + } - seqCanvas.repaint(); - } + void setSelectionAreaAtCursor(boolean topLeft) + { + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); - void setSelectionAreaAtCursor(boolean topLeft) + if (av.getSelectionGroup() != null) { - 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++) { - 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) { - int index = av.alignment.findIndex( sg.getSequenceAt(i) ); - if(index > max) - max = index; - if(index < min) - min = index; + max = index; } - - max ++; - - if(topLeft) + if (index < min) { - sg.setStartRes(seqCanvas.cursorX); - if(sg.getEndRes()seqCanvas.cursorX) - sg.setStartRes(seqCanvas.cursorX); + } - max = seqCanvas.cursorY+1; - } + max++; - if(min>max) + if (topLeft) + { + sg.setStartRes(seqCanvas.cursorX); + if (sg.getEndRes() < seqCanvas.cursorX) { - // Only the user can do this - av.setSelectionGroup(null); + sg.setEndRes(seqCanvas.cursorX); } - else + + min = seqCanvas.cursorY; + } + else + { + sg.setEndRes(seqCanvas.cursorX); + if (sg.getStartRes() > seqCanvas.cursorX) { - // Now add any sequences between min and max - sg.sequences.clear(); - for (int i = min; i < max; i++) - { - sg.addSequence(av.alignment.getSequenceAt(i), false); - } + sg.setStartRes(seqCanvas.cursorX); } + + max = seqCanvas.cursorY + 1; } - if (av.getSelectionGroup() == null) + if (min > max) { - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(seqCanvas.cursorX); - sg.setEndRes(seqCanvas.cursorX); - sg.addSequence(sequence, false); - av.setSelectionGroup(sg); + // Only the user can do this + av.setSelectionGroup(null); + } + else + { + // Now add any sequences between min and max + sg.getSequences(null).clear(); + for (int i = min; i < max; i++) + { + sg.addSequence(av.alignment.getSequenceAt(i), false); + } } - - - ap.repaint(); } - void insertGapAtCursor(boolean group) + if (av.getSelectionGroup() == null) { - 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(); + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(seqCanvas.cursorX); + sg.setEndRes(seqCanvas.cursorX); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); } - void deleteGapAtCursor(boolean group) + ap.repaint(); + } + + void insertGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(true, seqCanvas.cursorX + getKeyboardNo(keyboardNo1)); + endEditing(); + } + + void deleteGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX + getKeyboardNo(keyboardNo1); + editSequence(false, seqCanvas.cursorX); + endEditing(); + } + + void numberPressed(char value) + { + if (keyboardNo1 == null) { - 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(); + keyboardNo1 = new StringBuffer(); } - void numberPressed(char value) + if (keyboardNo2 != null) { - if(keyboardNo1==null) - keyboardNo1 = new StringBuffer(); - - if(keyboardNo2!=null) - keyboardNo2.append(value); - else - keyboardNo1.append(value); + keyboardNo2.append(value); } - - int getKeyboardNo(StringBuffer kb) + else { - if(kb==null) - return 1; - else - return Integer.parseInt(kb.toString()); + keyboardNo1.append(value); } + } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseReleased(MouseEvent evt) + int getKeyboardNo(StringBuffer kb) + { + if (kb == null) { - mouseDragging = false; - mouseWheelPressed = false; - - if (!editingSeqs) - { - doMouseReleasedDefineMode(evt); - return; - } + return 1; + } + else + { + return Integer.parseInt(kb.toString()); + } + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseReleased(MouseEvent evt) + { + mouseDragging = false; + mouseWheelPressed = false; + + if (!editingSeqs) + { + doMouseReleasedDefineMode(evt); + return; + } - editOccurred(); + endEditing(); - endEditing(); - ap.repaint(); - } + ap.repaint(); + } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mousePressed(MouseEvent evt) + { + lastMousePress = evt.getPoint(); + if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + { + mouseWheelPressed = true; + return; + } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mousePressed(MouseEvent evt) + if (evt.isShiftDown() || evt.isAltDown() || + evt.isControlDown()) { - if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + if (evt.isAltDown() || evt.isControlDown()) { - mouseWheelPressed = true; - return; + groupEditing = true; } + editingSeqs = true; + } + else + { + doMousePressedDefineMode(evt); + return; + } - if (evt.isShiftDown() || evt.isAltDown() || - evt.isControlDown()) - { - if (evt.isAltDown() || evt.isControlDown()) - { - groupEditing = true; - } - editingSeqs = true; - } - else - { - doMousePressedDefineMode(evt); - return; - } + 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; + } - int seq = findSeq(evt); - int res = findRes(evt); + return; + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseMoved(MouseEvent evt) + { + if (editingSeqs) + { + // This is because MacOSX creates a mouseMoved + // If control is down, other platforms will not. + mouseDragged(evt); + } - if(seq<0 || res<0) - return; + int res = findRes(evt); + int seq = findSeq(evt); - ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", - av.alignment, HistoryItem.EDIT)); + if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) + { + return; + } - if ((seq < av.getAlignment().getHeight()) && - (res < av.getAlignment().getSequenceAt(seq).getLength())) - { - startseq = seq; - lastres = res; - } - else - { - startseq = -1; - lastres = -1; - } + SequenceI sequence = av.getAlignment().getSequenceAt(seq); - return; + if (res > sequence.getLength()) + { + return; } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseMoved(MouseEvent evt) + if (seqCanvas.pdbCanvas != null && sequence == seqCanvas.pdbCanvas.sequence) { - if (editingSeqs) - { - // This is because MacOSX creates a mouseMoved - // If control is down, other platforms will not. - mouseDragged(evt); - } + seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); + } - int res = findRes(evt); - int seq = findSeq(evt); + setStatusMessage(sequence, res, seq); + tooltipText.setLength(6); // Cuts the buffer back to - if(res<0 || seq<0 || seq >= av.getAlignment().getHeight()) - return; + 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 (tooltipText.length() > 6) + { + tooltipText.append("
"); + } - SequenceI sequence = av.getAlignment().getSequenceAt(seq); + if (!groups[g].getName().startsWith("JTreeGroup") && + !groups[g].getName().startsWith("JGroup")) + { + tooltipText.append(groups[g].getName()); + } - if (res > sequence.getLength()) - { - return; + if (groups[g].getDescription() != null) + { + tooltipText.append(": " + groups[g].getDescription()); + } + } } + } - if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) + // use aa to see if the mouse pointer is on a + if (av.showSequenceFeatures) + { + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), sequence.findPosition(res)); + + if (features != null) { - seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); - } + 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 (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("
"); + } - setStatusMessage(sequence, res, seq); + tooltipText.append(features[i].getType() + " " + + features[i].begin); + if (features[i].begin != features[i].end) + { + tooltipText.append(" " + features[i].end); + } - // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) - { - SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures(); - if(features!=null) + if (features[i].getDescription() != null + && !features[i].description.equals(features[i].getType())) { - StringBuffer sbuffer = new StringBuffer(""); + tmpString = features[i].getDescription(); + int startTag = tmpString.toUpperCase().indexOf(""); + if (startTag > -1) + { + tmpString = tmpString.substring(startTag + 6); + } + int endTag = tmpString.toUpperCase().indexOf(""); + if (endTag > -1) + { + tmpString = tmpString.substring(0, endTag); + } + endTag = tmpString.toUpperCase().indexOf(""); + if (endTag > -1) + { + tmpString = tmpString.substring(0, endTag); + } - for (int i = 0; i < features.length; i++) + 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(">", ">"); + + tooltipText.append("; "); + tooltipText.append(tmpString); - if ( (features[i].getBegin() <= sequence.findPosition(res)) && - (features[i].getEnd() >= sequence.findPosition(res))) + } + else { - if(av.featuresDisplayed==null - || !av.featuresDisplayed.containsKey(features[i].getType())) - continue; - - - if (features[i].getType().equals("disulfide bond")) - { - 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()); - } - } - else - { - if (sbuffer.length() > 6) - sbuffer.append("
"); - if(features[i].featureGroup!=null) - sbuffer.append(features[i].featureGroup+";"); - - sbuffer.append(features[i].getType()); - - 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) - { - sbuffer.append("; (" + features[i].getStatus() + ")"); - } - } + 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") + ")"); + } + } - sbuffer.append(""); - if(sbuffer.length()==13) // - setToolTipText(""); - else - setToolTipText(sbuffer.toString()); + if (features[i].links != null) + { + tooltipText.append(" "); } - else - setToolTipText(""); + + } } + } } - void setStatusMessage(SequenceI sequence, int res, int seq) + if (tooltipText.length() == 6) // + { + setToolTipText(null); + } + else { - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + - sequence.getName()); + tooltipText.append(""); + setToolTipText(tooltipText.toString()); + } + // else + // setToolTipText(null); + } - 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: "); - } + 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) { - - if (obj != "") - { - text.append(obj + " (" + sequence.findPosition(res) + - ")"); - } + text.append(" Nucleotide: "); } - ap.alignFrame.statusBar.setText(text.toString()); - } - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void mouseDragged(MouseEvent evt) + else { - if (!editingSeqs) + obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); + if (obj != null) { - doMouseDraggedDefineMode(evt); - return; + text.append(" Residue: "); } + } - int res = findRes(evt); + if (obj != null) + { - if (res < 0) - { - res = 0; + if (obj != "") + { + text.append(obj + " (" + sequence.findPosition(res) + + ")"); + } + } + ap.alignFrame.statusBar.setText(text.toString()); + + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + 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 ((lastres == -1) || (lastres == res)) + if (fontSize < 1) { - return; + fontSize = 1; } - if ( (res < av.getAlignment().getWidth()) && (res < lastres)) + 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) { - // dragLeft, delete gap - editSequence(false, res); + av.charWidth--; + } + else if (evt.getX() > lastMousePress.getX()) + { + av.charWidth++; } - else - editSequence(true, res); - mouseDragging = true; - if(scrollThread!=null) - scrollThread.setEvent(evt); + ap.repaint(); + } + + FontMetrics fm = getFontMetrics(av.getFont()); + av.validCharWidth = fm.charWidth('M') <= av.charWidth; + lastMousePress = evt.getPoint(); + + return; } - synchronized void editSequence(boolean insertGap, int startres) + if (!editingSeqs) { - int fixedLeft = -1; - int fixedRight = -1; - boolean fixedColumns = false; - SequenceGroup sg = av.getSelectionGroup(); + doMouseDraggedDefineMode(evt); + return; + } - if(groupEditing && sg==null) - return; + int res = findRes(evt); - if (!groupEditing && av.hasHiddenRows) - { - //This needs to check all the sequences in a group edit,m - // not just the startseq - if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null) - { - groupEditing = true; - } - } + if (res < 0) + { + res = 0; + } - SequenceI seq = av.alignment.getSequenceAt(startseq); - StringBuffer message = new StringBuffer(); - if (groupEditing) - message.append("Edit group:"); - else - message.append("Edit sequence: "+seq.getName()); + if ( (lastres == -1) || (lastres == res)) + { + return; + } - if(insertGap) - message.append(" insert "); - else - message.append(" delete "); + if ( (res < av.getAlignment().getWidth()) && (res < lastres)) + { + // dragLeft, delete gap + editSequence(false, res); + } + else + { + editSequence(true, res); + } - message.append(Math.abs(startres-lastres)+" gaps."); - ap.alignFrame.statusBar.setText(message.toString()); + mouseDragging = true; + if (scrollThread != null) + { + scrollThread.setEvent(evt); + } + } - //Are we editing within a selection group? - if (groupEditing - || (sg != null && sg.sequences.contains(seq))) - { - fixedColumns = true; + synchronized void editSequence(boolean insertGap, int startres) + { + int fixedLeft = -1; + int fixedRight = -1; + boolean fixedColumns = false; + SequenceGroup sg = av.getSelectionGroup(); - fixedLeft = sg.getStartRes(); - fixedRight = sg.getEndRes(); + SequenceI seq = av.alignment.getSequenceAt(startseq); - if ( (startres < fixedLeft && lastres >= fixedLeft) - || (startres >= fixedLeft && lastres < fixedLeft) - || (startres > fixedRight && lastres <=fixedRight) - || (startres <= fixedRight && lastres > fixedRight)) - { - endEditing(); - return; - } + //No group, but the sequence may represent a group + if (!groupEditing && av.hasHiddenRows) + { + if (av.hiddenRepSequences != null + && av.hiddenRepSequences.containsKey(seq)) + { + sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + groupEditing = true; + } + } - if (fixedLeft > startres) - { - fixedRight = fixedLeft - 1; - fixedLeft = 0; - } - else if (fixedRight < startres) - { - fixedLeft = fixedRight; - fixedRight = -1; - } + StringBuffer message = new StringBuffer(); + if (groupEditing) + { + message.append("Edit group:"); + if (editCommand == null) + { + 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); + } + } + + if (insertGap) + { + message.append(" insert "); + } + else + { + message.append(" delete "); + } + + 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; + + //sg might be null as the user may only see 1 sequence, + //but the sequence represents a group + if (sg == null) + { + if (av.hiddenRepSequences == null + || !av.hiddenRepSequences.containsKey(seq)) + { + endEditing(); + return; } + 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; + } - if(av.hasHiddenColumns) + //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); + //Selection spans a hidden region + if (fixedLeft < y1 && (fixedRight > y2 || fixedRight == -1)) + { + if (startres >= y2) { - fixedColumns = true; - int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); - int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + fixedLeft = y2; + } + else + { + fixedRight = y2 - 1; + } + } + } - if( ( insertGap && startres>y1 && lastresy2) ) - { - endEditing(); - return; - } + 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); + } - if(fixedRightfixedLeft && fixedLeft==-1) - fixedLeft = y1; + // 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(); } - if (groupEditing) + // 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; - /*if (av.hasHiddenRows) + for (g = 0; g < groupSize; g++) { - //sg might be null as the user may only see 1 sequence - if (sg == null) + for (int j = 0; j < startres - lastres; j++) { - sg = new SequenceGroup(); - sg.addSequence(av.alignment.getSequenceAt(startseq), false); - } - - 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) + if (!jalview.util.Comparison.isGap( + groupSeqs[g].getCharAt(fixedRight - j))) { - for (int h = 0; h < seq.getHiddenSequences().getSize(); h++) - tmp.addSequence(seq.getHiddenSequences().getSequenceAt(h), - false); + blank = false; + break; } } - - sg = tmp; - }*/ - // int blankColumn = -1; - - - // drag to right - if (insertGap) + } + if (blank) { - //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()) - { - sg.setEndRes(av.alignment.getWidth() + startres - lastres); - fixedRight = sg.getEndRes(); - } + break; + } + } - // 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--) + if (!blank) + { + if (sg.getSize() == av.alignment.getHeight()) + { + if ( (av.hasHiddenColumns + && + startres < av.getColumnSelection().getHiddenBoundaryRight(startres))) { - blank = true; - for (int s = 0; s < sg.getSize(); s++) - { - seq = sg.getSequenceAt(s); - for (int j = 0; j < startres - lastres; j++) - { - if (!jalview.util.Comparison.isGap( - seq.getCharAt(fixedRight - j))) - { - blank = false; - break; - } - } - } - if (blank) - break; + endEditing(); + return; } - if (!blank) + int alWidth = av.alignment.getWidth(); + if (av.hasHiddenRows) { - if(sg.getSize() == av.alignment.getHeight()) - { - //We can still insert gaps if the selectionGroup - //contains all the sequences - sg.setEndRes(sg.getEndRes()+1+startres-lastres); - fixedRight = av.alignment.getWidth()+startres-lastres; - } - else + int hwidth = av.alignment.getHiddenSequences().getWidth(); + if (hwidth > alWidth) { - endEditing(); - return; + 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; } + } + } + // 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++) + { + for (int j = startres; j < lastres; j++) { - /// Are we able to delete? - // ie are all columns blank? - - for (int s = 0; s < sg.getSize(); s++) + if (groupSeqs[g].getLength() <= j) { - seq = sg.getSequenceAt(s); - - for (int j = startres; j < lastres; 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(); i++) + if (insertGap) + { + // dragging to the right + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j < startres; j++) + { + insertChar(j, groupSeqs, fixedRight); + } + } + 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--) { - seq = sg.getSequenceAt(i); + deleteChar(startres, groupSeqs, fixedRight); + } + } + else + { + editCommand.appendEdit(EditCommand.DELETE_GAP, + groupSeqs, + startres, lastres - startres, + av.alignment, + true); + } - 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); - } - } - } + } + } + else /////Editing a single sequence/////////// + { + if (insertGap) + { + // dragging to the right + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j < startres; j++) + { + insertChar(j, new SequenceI[] + {seq}, fixedRight); } } - else /////Editing a single sequence/////////// + else + { + editCommand.appendEdit(EditCommand.INSERT_GAP, + new SequenceI[] + {seq}, + lastres, startres - lastres, + av.alignment, + true); + } + } + else + { + // dragging to the left + if (fixedColumns && fixedRight != -1) { - if (insertGap) + for (int j = lastres; j > startres; j--) { - // dragging to the right - for (int j = lastres; j < startres; j++) + if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) { - if (fixedColumns && fixedRight != -1) - { - if (sg.getStartRes() == 0 - && sg.getEndRes() + 1 == av.alignment.getWidth() - && !jalview.util.Comparison.isGap(seq.getCharAt(fixedRight))) - { - //Single sequence edit, whole sequence selected, - //extend the selection group - sg.setEndRes(av.alignment.getWidth() -1 + startres - lastres); - fixedColumns = false; - insertChar(j, seq); - } - else - insertChar(j, seq, fixedRight); - } - else - insertChar(j, seq); + 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; m < lastres; m++) { - // dragging to the left - for (int j = lastres; j > startres; j--) + if (!jalview.util.Comparison.isGap(seq.getCharAt(m))) { - if (fixedColumns && fixedRight != -1) - { - deleteChar(startres, seq, fixedRight); - } - else - { - deleteChar(startres, seq); - } + break; } + max++; } - } - lastres = startres; - seqCanvas.repaint(); + if (max > 0) + { + editCommand.appendEdit(EditCommand.DELETE_GAP, + new SequenceI[] + {seq}, + startres, max, + av.alignment, + true); + } + } + } } + 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; @@ -930,500 +1250,529 @@ public class SeqPanel extends JPanel implements MouseListener, 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); + + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + j, 1, av.alignment, + true); + + } + + void deleteChar(int j, SequenceI[] seq, int fixedColumn) + { + + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + j, 1, av.alignment, true); + + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + fixedColumn, 1, av.alignment, true); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) + { + if (oldSeq < 0) + { + oldSeq = 0; + } - seq.deleteCharAt(blankColumn); - seq.insertCharAt(j, av.getGapCharacter()); - seqEditOccurred = true; + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseExited(MouseEvent e) + { + if (av.getWrapAlignment()) + { + return; } - void deleteChar(int j, SequenceI seq, int fixedColumn) + if (mouseDragging) { - if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) + scrollThread = new ScrollThread(); + } + } + + 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) { - ap.alignFrame.statusBar.setText( - "End editing: Tried removing residue " + seq.getCharAt(j)); - return; + av.setSelectionGroup(null); } - seq.deleteCharAt(j); - seq.insertCharAt(fixedColumn, av.getGapCharacter()); - seqEditOccurred = true; - } + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), + sequence.findPosition(findRes(evt)) + ); - /** - * DOCUMENT ME! - * - * @param j DOCUMENT ME! - * @param seq DOCUMENT ME! - */ - void deleteChar(int j, SequenceI seq) - { - if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) + if (features != null && features.length > 0) { - ap.alignFrame.statusBar.setText( - "End editing: Tried removing residue " + seq.getCharAt(j)); - return; + 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); - seq.deleteCharAt(j); - seqEditOccurred = true; - seqCanvas.repaint(); + seqCanvas.highlightSearchResults(null); + } } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseEntered(MouseEvent e) - { - if(oldSeq < 0) - oldSeq = 0; + } - if (scrollThread != null) - { - scrollThread.running = false; - scrollThread = null; - } - } + public void mouseWheelMoved(MouseWheelEvent e) + { + e.consume(); + /* if (mouseWheelPressed) + { + Font font = av.getFont(); + int fontSize = font.getSize(); + if (e.getWheelRotation() > 0 && fontSize < 51) + fontSize++; + else if (fontSize > 1) + fontSize--; - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void mouseExited(MouseEvent e) - { - if (av.getWrapAlignment()) - { - return; - } - if (mouseDragging) - { - scrollThread = new ScrollThread(); - } - } - public void mouseClicked(MouseEvent evt) - {} + av.setFont(new Font(font.getName(), font.getStyle(), fontSize)); - public void mouseWheelMoved(MouseWheelEvent e) + ap.fontChanged(); + } + else*/ { - e.consume(); - if (mouseWheelPressed) + if (e.getWheelRotation() > 0) { - Font font = av.getFont(); - int fontSize = font.getSize(); - if (e.getWheelRotation() > 0 && fontSize < 51) - fontSize++; - else if (fontSize > 1) - fontSize--; - - av.setFont(new Font(font.getName(), font.getStyle(), fontSize)); - ap.fontChanged(); + ap.scrollUp(false); } else { - if (e.getWheelRotation() > 0) - ap.scrollUp(false); - else - ap.scrollUp(true); + ap.scrollUp(true); } - } + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMousePressedDefineMode(MouseEvent evt) + { + int res = findRes(evt); + int seq = findSeq(evt); + oldSeq = seq; + startWrapBlock = wrappedBlock; - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - */ - void editOccurred() + if (av.wrapAlignment && seq > av.alignment.getHeight()) { - if (!seqEditOccurred) - { - ap.alignFrame.historyList.pop(); - ap.alignFrame.updateEditMenuBar(); - } + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Cannot edit annotations in wrapped view.", + "Wrapped view - no edit", + JOptionPane.WARNING_MESSAGE); + return; + } - endEditing(); + if (seq < 0 || res < 0) + { + return; + } - av.firePropertyChange("alignment", null,av.getAlignment().getSequences()); + SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); + if ( (sequence == null) || (res > sequence.getLength())) + { + return; } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMousePressedDefineMode(MouseEvent evt) - { - int res = findRes(evt); - int seq = findSeq(evt); - oldSeq = seq; + stretchGroup = av.getSelectionGroup(); - startWrapBlock=wrappedBlock; + if (stretchGroup == null) + { + stretchGroup = av.alignment.findGroup(sequence); - if(av.wrapAlignment && seq>av.alignment.getHeight()) + if ( (stretchGroup != null) && (res > stretchGroup.getStartRes()) && + (res < stretchGroup.getEndRes())) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Cannot edit annotations in wrapped view.", - "Wrapped view - no edit", - JOptionPane.WARNING_MESSAGE); - return; + av.setSelectionGroup(stretchGroup); } + else + { + stretchGroup = null; + } + } + else if (!stretchGroup.getSequences(null).contains(sequence) || + (stretchGroup.getStartRes() > res) || + (stretchGroup.getEndRes() < res)) + { + stretchGroup = null; - if(seq<0 || res<0) - return; - - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); - - if ((sequence == null) || (res > sequence.getLength())) - { - return; - } - - stretchGroup = av.getSelectionGroup(); + SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); - if (stretchGroup == null) + if (allGroups != null) + { + for (int i = 0; i < allGroups.length; i++) { - stretchGroup = av.alignment.findGroup(sequence); - - if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) && - (res < stretchGroup.getEndRes())) - { - av.setSelectionGroup(stretchGroup); - } - else - { - stretchGroup = null; - } + if ( (allGroups[i].getStartRes() <= res) && + (allGroups[i].getEndRes() >= res)) + { + stretchGroup = allGroups[i]; + break; + } } - else if (!stretchGroup.sequences.contains(sequence) || - (stretchGroup.getStartRes() > res) || - (stretchGroup.getEndRes() < res)) - { - stretchGroup = null; + } - SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); + av.setSelectionGroup(stretchGroup); - if (allGroups != null) - { - for (int i = 0; i < allGroups.length; i++) - { - if ((allGroups[i].getStartRes() <= res) && - (allGroups[i].getEndRes() >= res)) - { - stretchGroup = allGroups[i]; - av.setSelectionGroup(stretchGroup); - - break; - } - } - } - } + } - if (av.cursorMode) + 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) { - seqCanvas.cursorX = findRes(evt); - seqCanvas.cursorY = findSeq(evt); - seqCanvas.repaint(); - return; + 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 (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"); - } - - 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()); + if (av.cursorMode) + { + seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorY = findSeq(evt); + seqCanvas.repaint(); + return; + } - // edit the properties of existing group - } + if (stretchGroup == null) + { + //Only if left mouse button do we want to change group sizes - if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) - { - // Edit end res position of selected group - changeEndRes = true; - } - else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) - { - // Edit end res position of selected group - changeStartRes = true; - } + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; - stretchGroup.getWidth(); + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, + av.getGlobalColourScheme(), + "Background"); + } - seqCanvas.repaint(); + 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)) + { + // Edit end res position of selected group + changeStartRes = true; + } + stretchGroup.getWidth(); } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMouseReleasedDefineMode(MouseEvent evt) + seqCanvas.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseReleasedDefineMode(MouseEvent evt) + { + if (stretchGroup == null) { - if (stretchGroup == null) - { - return; - } + return; + } + if (stretchGroup.cs != null) + { + if (stretchGroup.cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX( + stretchGroup.getSequences(av.hiddenRepSequences), + stretchGroup.getWidth()); + } - if(stretchGroup.cs!=null) - { - if (stretchGroup.cs instanceof ClustalxColourScheme) - { - ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup. - sequences, - 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 - { - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, - stretchGroup.getName()); - } - } - changeEndRes = false; - changeStartRes = false; - stretchGroup = null; - PaintRefresher.Refresh(av.alignment); + if (stretchGroup.cs.conservationApplied()) + { + SliderPanel.setConservationSlider(ap, stretchGroup.cs, + stretchGroup.getName()); + } + else + { + SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, + stretchGroup.getName()); + } + } + changeEndRes = false; + changeStartRes = false; + stretchGroup = null; + + PaintRefresher.Refresh(this, av.getSequenceSetId()); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseDraggedDefineMode(MouseEvent evt) + { + int res = findRes(evt); + int y = findSeq(evt); + + if (wrappedBlock != startWrapBlock) + { + return; } - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMouseDraggedDefineMode(MouseEvent evt) + if (stretchGroup == null) { - int res = findRes(evt); - int y = findSeq(evt); + return; + } - if(wrappedBlock!=startWrapBlock) - return; + if (res >= av.alignment.getWidth()) + { + res = av.alignment.getWidth() - 1; + } - if (stretchGroup == null) - { - return; - } + 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.getStartRes()) + { + res = av.getStartRes(); + } - if(y > av.alignment.getHeight()) - { - y = av.alignment.getHeight() -1; - } - if(res> av.alignment.getWidth()) - { - res = av.alignment.getWidth()-1; - } + if (changeEndRes) + { + if (res > (stretchGroup.getStartRes() - 1)) + { + stretchGroup.setEndRes(res); + } + } + else if (changeStartRes) + { + if (res < (stretchGroup.getEndRes() + 1)) + { + stretchGroup.setStartRes(res); + } + } - 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; - } + int dragDirection = 0; - if (res < av.getStartRes()) - { - res = av.getStartRes(); - } + if (y > oldSeq) + { + dragDirection = 1; + } + else if (y < oldSeq) + { + dragDirection = -1; + } - if (changeEndRes) - { - if (res > (stretchGroup.getStartRes() - 1)) - { - stretchGroup.setEndRes(res); - } - } - else if (changeStartRes) - { - if (res < (stretchGroup.getEndRes() + 1)) - { - stretchGroup.setStartRes(res); - } - } + 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) - { - dragDirection = -1; - } + if (oldSeq < 0) + { + break; + } + Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) + if (stretchGroup.getSequences(null).contains(nextSeq)) + { + stretchGroup.deleteSequence(seq, false); + } + else + { + if (seq != null) { - // 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.sequences.contains(nextSeq)) - { - stretchGroup.deleteSequence(seq, false); - } - else - { - if (seq != null) - { - stretchGroup.addSequence(seq, false); - } - - stretchGroup.addSequence(nextSeq, false); - } + stretchGroup.addSequence(seq, false); } - if(oldSeq < 0) - oldSeq = -1; + stretchGroup.addSequence(nextSeq, false); + } + } - mouseDragging = true; + if (oldSeq < 0) + { + oldSeq = -1; + } - if (scrollThread != null) - { - scrollThread.setEvent(evt); - } + mouseDragging = true; - seqCanvas.repaint(); + if (scrollThread != null) + { + scrollThread.setEvent(evt); } - void scrollCanvas(MouseEvent evt) + seqCanvas.repaint(); + } + + void scrollCanvas(MouseEvent evt) + { + if (evt == null) { - if(evt==null) + if (scrollThread != null) { - if(scrollThread!=null) - { - scrollThread.running = false; - scrollThread = null; - } - mouseDragging = false; + scrollThread.running = false; + scrollThread = null; } - else + mouseDragging = false; + } + else + { + if (scrollThread == null) { - if (scrollThread == null) - scrollThread = new ScrollThread(); - - mouseDragging = true; - scrollThread.setEvent(evt); + scrollThread = new ScrollThread(); } + mouseDragging = true; + scrollThread.setEvent(evt); } + } + + // this class allows scrolling off the bottom of the visible alignment + class ScrollThread + extends Thread + { + MouseEvent evt; + boolean running = false; - // this class allows scrolling off the bottom of the visible alignment - class ScrollThread extends Thread + public ScrollThread() { - MouseEvent evt; - boolean running = false; + start(); + } - public ScrollThread() - { - start(); - } + public void setEvent(MouseEvent e) + { + evt = e; + } + + public void stopScrolling() + { + running = false; + } + + public void run() + { + running = true; - public void setEvent(MouseEvent e) + while (running) + { + if (evt != null) { - evt = e; + if (mouseDragging && (evt.getY() < 0) && + (av.getStartSeq() > 0)) + { + running = ap.scrollUp(true); + } + + if (mouseDragging && (evt.getY() >= getHeight()) && + (av.alignment.getHeight() > av.getEndSeq())) + { + running = ap.scrollUp(false); + } + + if (mouseDragging && (evt.getX() < 0)) + { + running = ap.scrollRight(false); + } + else if (mouseDragging && (evt.getX() >= getWidth())) + { + running = ap.scrollRight(true); + } } - public void stopScrolling() + try { - running = false; + Thread.sleep(20); } - - public void run() + catch (Exception ex) { - running = true; - - while (running) - { - if (evt != null) - { - if (mouseDragging && (evt.getY() < 0) && - (av.getStartSeq() > 0)) - { - running = ap.scrollUp(true); - } - - if (mouseDragging && (evt.getY() >= getHeight()) && - (av.alignment.getHeight() > av.getEndSeq())) - { - running = ap.scrollUp(false); - } - - if (mouseDragging && (evt.getX() < 0)) - { - running = ap.scrollRight(false); - } - else if (mouseDragging && (evt.getX() >= getWidth())) - { - running = ap.scrollRight(true); - } - } - - try - { - Thread.sleep(20); - } - catch (Exception ex) - { - } - } } + } } + } }