X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=a4c22795c7878bc5b190b21d474ae7534c7edea1;hb=ecb5ab32cb7599f6665117ad4e25c61f0a650720;hp=8486ac1f59f78c5ef76080d5a16f2d3367a36ed6;hpb=ce728f87f1f43be3041ef02f7f2cc2e39314711a;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 8486ac1..a4c2279 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -18,18 +18,14 @@ */ package jalview.gui; -import jalview.analysis.*; - import jalview.datamodel.*; - +import jalview.commands.EditCommand; import jalview.schemes.*; import java.awt.*; import java.awt.event.*; - -import java.util.*; - import javax.swing.*; +import java.util.Vector; /** @@ -38,236 +34,412 @@ import javax.swing.*; * @author $author$ * @version $Revision$ */ -public class SeqPanel extends JPanel +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; - int startEdit = -1; - int endEdit = -1; - protected AlignViewport av; - - // if character is inserted or deleted, we will need to recalculate the conservation - int seqEditOccurred = -1; - 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; + /** 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); + } + } - /** - * Creates a new SeqPanel object. - * - * @param avp DOCUMENT ME! - * @param p DOCUMENT ME! - */ - public SeqPanel(AlignViewport avp, AlignmentPanel p) + int startWrapBlock = -1; + int wrappedBlock = -1; + int findRes(MouseEvent evt) + { + int res = 0; + int x = evt.getX(); + + if (av.wrapAlignment) { - 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); + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; - ap = p; + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); - addMouseMotionListener(new MouseMotionAdapter() - { - public void mouseMoved(MouseEvent evt) - { - doMouseMoved(evt); - } + int y = evt.getY(); + y -= hgap; + x -= seqCanvas.LABEL_WEST; - public void mouseDragged(MouseEvent evt) - { - if (editingSeqs) - { - doMouseDragged(evt); - } - else - { - doMouseDraggedDefineMode(evt); - } - } - }); + int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); + if (cwidth < 1) + return 0; - addMouseWheelListener(new MouseWheelListener() - { - public void mouseWheelMoved(MouseWheelEvent e) - { + wrappedBlock = y / cHeight; + wrappedBlock += av.getStartRes() / cwidth; - if (mouseWheelPressed) - { - Font font = av.getFont(); - int fontSize = font.getSize(); - if (e.getWheelRotation() > 0 && fontSize < 30) - fontSize++; - else if (fontSize > 1) - fontSize--; - - av.setFont(new Font(font.getName(), font.getStyle(), fontSize)); - ap.fontChanged(); - } - else - { - if (e.getWheelRotation() > 0) - ap.scrollUp(false); - else - ap.scrollUp(true); - } + res = wrappedBlock * cwidth + x / av.getCharWidth(); - } - }); + } + else + { + res = (x / av.getCharWidth()) + av.getStartRes(); + } + if (av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); - addMouseListener(new MouseAdapter() - { - public void mouseReleased(MouseEvent evt) - { - mouseWheelPressed = false; + return res; - if (editingSeqs) - { - doMouseReleased(evt); - } - else - { - doMouseReleasedDefineMode(evt); - } - } + } - public void mousePressed(MouseEvent evt) - { - if( javax.swing.SwingUtilities.isMiddleMouseButton(evt)) - { - mouseWheelPressed = true; - return; - } + int findSeq(MouseEvent evt) + { + int seq = 0; + int y = evt.getY(); - if (evt.isShiftDown() || evt.isAltDown() || - evt.isControlDown()) - { - if (evt.isAltDown() || evt.isControlDown()) - { - groupEditing = true; - } + if (av.wrapAlignment) + { + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; - editingSeqs = true; - doMousePressed(evt); - } - else - { - doMousePressedDefineMode(evt); - } - } + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); - public void mouseExited(MouseEvent evt) - { - if (editingSeqs) - { - return; - } + y -= hgap; - doMouseExitedDefineMode(evt); - } + seq = Math.min( (y % cHeight) / av.getCharHeight(), + av.alignment.getHeight() - 1); + } + else + { + seq = Math.min( (y / av.getCharHeight()) + av.getStartSeq(), + av.alignment.getHeight() - 1); + } - public void mouseEntered(MouseEvent evt) - { - if (editingSeqs) - { - return; - } + return seq; + } - doMouseEnteredDefineMode(evt); - } - }); + SequenceFeature[] findFeaturesAtRes(SequenceI sequence, int res) + { + Vector tmp = new Vector(); + SequenceFeature[] features = sequence.getSequenceFeatures(); + if (features != null) + { + for (int i = 0; i < features.length; i++) + { + if (av.featuresDisplayed == null + || !av.featuresDisplayed.containsKey(features[i].getType())) + continue; + + if ( (features[i].getBegin() <= res) && + (features[i].getEnd() >= res)) + { + tmp.addElement(features[i]); + } + } } - int startWrapBlock=-1; - int wrappedBlock=-1; - int findRes(MouseEvent evt) + features = new SequenceFeature[tmp.size()]; + for(int i=0; i= res) + { + if (av.featuresDisplayed.containsKey(sf.getType())) + { + allFeatures.addElement(sf); + } + } + index++; + } + } + return allFeatures; + } - if (av.wrapAlignment) + void endEditing() + { + if (editCommand!=null && editCommand.getSize() > 0) + { + ap.alignFrame.addHistoryItem(editCommand); + av.firePropertyChange("alignment", null, + av.getAlignment().getSequences()); + } + + startseq = -1; + lastres = -1; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + editCommand = null; + } + + void setCursorRow() { + seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } - int hgap = av.charHeight; - if (av.scaleAboveWrapped) - hgap += av.charHeight; + void setCursorColumn() + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } - int cHeight = av.getAlignment().getHeight() * av.charHeight - + hgap + seqCanvas.getAnnotationHeight(); + void setCursorRowAndColumn() + { + if(keyboardNo2==null) + { + keyboardNo2 = new StringBuffer(); + } + else + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; + seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1; + scrollToVisible(); + } + } - int y = evt.getY(); - y -= hgap; - x -= seqCanvas.LABEL_WEST; + 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; - int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); + if (seqCanvas.cursorY < 0) + seqCanvas.cursorY = 0; + else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) + seqCanvas.cursorY = av.alignment.getHeight() - 1; - wrappedBlock = y / cHeight; - wrappedBlock += av.getStartRes() / cwidth; - res = wrappedBlock * cwidth + x / av.getCharWidth(); + endEditing(); + if(av.wrapAlignment) + { + ap.scrollToWrappedVisible(seqCanvas.cursorX); + } + else + { + while (seqCanvas.cursorY < av.startSeq) + { + ap.scrollUp(true); + } + while (seqCanvas.cursorY + 1 > av.endSeq) + { + ap.scrollUp(false); + } + if (!av.wrapAlignment) + { + while (seqCanvas.cursorX < av.startRes) + { + if (!ap.scrollRight(false)) + break; + } + while (seqCanvas.cursorX > av.endRes) + { + if (!ap.scrollRight(true)) + break; + } + } + } + setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), + seqCanvas.cursorX, seqCanvas.cursorY); + seqCanvas.repaint(); } - else + + void setSelectionAreaAtCursor(boolean topLeft) { - res = (x / av.getCharWidth()) + av.getStartRes(); - } + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); - return res; + 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 ++; - int findSeq(MouseEvent evt) - { + if(topLeft) + { + sg.setStartRes(seqCanvas.cursorX); + if(sg.getEndRes()seqCanvas.cursorX) + sg.setStartRes(seqCanvas.cursorX); - if (av.wrapAlignment) - { - int hgap = av.charHeight; - if (av.scaleAboveWrapped) - hgap += av.charHeight; + max = seqCanvas.cursorY+1; + } + + if(min>max) + { + // Only the user can do this + av.setSelectionGroup(null); + } + else + { + // Now add any sequences between min and max + sg.getSequences(false).clear(); + for (int i = min; i < max; i++) + { + sg.addSequence(av.alignment.getSequenceAt(i), false); + } + } + } - int cHeight = av.getAlignment().getHeight() * av.charHeight - + hgap + seqCanvas.getAnnotationHeight(); + if (av.getSelectionGroup() == null) + { + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(seqCanvas.cursorX); + sg.setEndRes(seqCanvas.cursorX); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + } - y -= hgap; - seq = ( (y % cHeight) / av.getCharHeight()); - } - else - { - seq = (y / av.getCharHeight()) + av.getStartSeq(); - } + ap.repaint(); + } + + void insertGapAtCursor(boolean group) + { + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(true, seqCanvas.cursorX+getKeyboardNo(keyboardNo1)); + endEditing(); + } - return seq; - } + 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) + 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()); + } /** @@ -275,31 +447,53 @@ public class SeqPanel extends JPanel * * @param evt DOCUMENT ME! */ - public void doMouseReleased(MouseEvent evt) + public void mouseReleased(MouseEvent evt) { - if (seqEditOccurred > -1) - { - editOccurred(seqEditOccurred); - } + mouseDragging = false; + mouseWheelPressed = false; - startseq = -1; - lastres = -1; - seqEditOccurred = -1; - editingSeqs = false; - groupEditing = false; + if (!editingSeqs) + { + doMouseReleasedDefineMode(evt); + return; + } - ap.repaint(); + endEditing(); + + ap.repaint(); } + + /** * DOCUMENT ME! * * @param evt DOCUMENT ME! */ - public void doMousePressed(MouseEvent evt) + public void mousePressed(MouseEvent evt) { - ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", - av.alignment, HistoryItem.EDIT)); + lastMousePress = evt.getPoint(); + + if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + { + mouseWheelPressed = true; + 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); @@ -319,9 +513,6 @@ public class SeqPanel extends JPanel lastres = -1; } - startEdit = lastres; - endEdit = lastres; - return; } @@ -330,283 +521,746 @@ public class SeqPanel extends JPanel * * @param evt DOCUMENT ME! */ - public void doMouseMoved(MouseEvent evt) + public void mouseMoved(MouseEvent evt) { + if (editingSeqs) + { + // This is because MacOSX creates a mouseMoved + // If control is down, other platforms will not. + mouseDragged(evt); + } + int res = findRes(evt); int seq = findSeq(evt); + if(res<0 || seq<0 || seq >= av.getAlignment().getHeight()) return; - SequenceI sequence = av.getAlignment().getSequenceAt(seq); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + + if (res > sequence.getLength()) + { + return; + } + + if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) + { + seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); + } + + setStatusMessage(sequence, res, seq); + + // use aa to see if the mouse pointer is on a + if (av.showSequenceFeatures) + { + tooltipText.setLength(6); // Cuts the buffer back to + + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), sequence.findPosition(res)); + + if(features!=null) + { + for (int i = 0; i < features.length; i++) + { + if (features[i].getType().equals("disulfide bond")) + { + if (features[i].getBegin() == sequence.findPosition(res) + || features[i].getEnd() == sequence.findPosition(res)) + { + if (tooltipText.length() > 6) + tooltipText.append("
"); + tooltipText.append("disulfide bond " + features[i].getBegin() + ":" + + features[i].getEnd()); + if (features[i].links != null) + tooltipText.append(" "); + } + } + else + { + if (tooltipText.length() > 6) + tooltipText.append("
"); + + tooltipText.append(features[i].getType() + " " + + features[i].begin); + if (features[i].begin != features[i].end) + tooltipText.append(" " + features[i].end); + + if (features[i].getDescription() != null + && !features[i].description.equals(features[i].getType())) + { + 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); + } + + 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); + + } + else + tooltipText.append("; "+tmpString); + } + } + if (features[i].getValue("status") != null ) + { + String status = features[i].getValue("status").toString(); + if(status.length()>0) + tooltipText.append("; (" + features[i].getValue("status") + ")"); + } + + if (features[i].links != null) + tooltipText.append(" "); + + } + + // else if(features[i].begin==0 && features[i].end==0) + { + // seqSpecific.append(features[i].featureGroup+": " + // + features[i].getType()+" " + // +features[i].getDescription()+"
"); + + } + } + + if(tooltipText.length()==6) // + { + + setToolTipText(""); + } + else + { + tooltipText.append(""); + setToolTipText(tooltipText.toString()); + } + } + else + setToolTipText(""); + } + } + + void setStatusMessage(SequenceI sequence, int res, int seq) + { + StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + + sequence.getName()); + + Object obj = null; + if (av.alignment.isNucleotide()) + { + obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + + ""); + if (obj != null) + text.append(" Nucleotide: "); + } + else + { + obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + ""); + if (obj != null) + text.append(" Residue: "); + } + + if (obj != null) + { + + if (obj != "") + { + text.append(obj + " (" + sequence.findPosition(res) + + ")"); + } + } + ap.alignFrame.statusBar.setText(text.toString()); + + } + + /** + * DOCUMENT ME! + * + * @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(fontSize<1) + fontSize = 1; + + av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); + av.charWidth = oldWidth; + ap.fontChanged(); + } + else + { + if (evt.getX() < lastMousePress.getX() && av.charWidth > 1) + { + av.charWidth--; + } + else if (evt.getX() > lastMousePress.getX()) + { + av.charWidth++; + } + + ap.repaint(); + } + + FontMetrics fm = getFontMetrics(av.getFont()); + av.validCharWidth = fm.charWidth('M') <= av.charWidth; + + lastMousePress = evt.getPoint(); + + return; + } + + if (!editingSeqs) + { + doMouseDraggedDefineMode(evt); + return; + } + + int res = findRes(evt); + + if (res < 0) + { + res = 0; + } + + if ((lastres == -1) || (lastres == res)) + { + return; + } + + 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); + + } - if (res > sequence.getLength()) - { - return; - } + synchronized void editSequence(boolean insertGap, int startres) + { + int fixedLeft = -1; + int fixedRight = -1; + boolean fixedColumns = false; + SequenceGroup sg = av.getSelectionGroup(); - Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + - ""); - String aa = ""; - if (obj != null) + if (!groupEditing && av.hasHiddenRows) { - aa = obj.toString(); + if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null) + { + groupEditing = true; + } } - StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + - sequence.getName()); - - if (aa != "") + //No group, but the sequence may represent a group + if (groupEditing + && sg == null + && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null) { - text.append(" Residue: " + aa + " (" + - av.getAlignment().getSequenceAt(seq).findPosition(res) + ")"); + groupEditing = false; } - ap.alignFrame.statusBar.setText(text.toString()); - - // use aa to see if the mouse pointer is on a - if (av.showSequenceFeatures) + SequenceI seq = av.alignment.getSequenceAt(startseq); + StringBuffer message = new StringBuffer(); + if (groupEditing) { - Vector features = sequence.getSequenceFeatures(); - Enumeration e = features.elements(); - StringBuffer sbuffer = new StringBuffer(); - - while (e.hasMoreElements()) - { - SequenceFeature sf = (SequenceFeature) e.nextElement(); + 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 ((sf.getStart() <= sequence.findPosition(res)) && - (sf.getEnd() >= sequence.findPosition(res))) - { - if (sbuffer.length() > 0) - { - sbuffer.append("; "); - } + if(insertGap) + message.append(" insert "); + else + message.append(" delete "); - sbuffer.append(sf.getType() + " " + sf.getDescription()); + message.append(Math.abs(startres-lastres)+" gaps."); + ap.alignFrame.statusBar.setText(message.toString()); - if (sf.getStatus().length() > 0) - { - sbuffer.append(" (" + sf.getStatus() + ")"); - } - } - } - this.setToolTipText(sbuffer.toString()); - } - } + //Are we editing within a selection group? + if (groupEditing + || (sg != null && sg.getSequences(true).contains(seq))) + { + fixedColumns = true; - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void doMouseDragged(MouseEvent evt) - { - // If we're dragging we're editing - int res = findRes(evt); + //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); + } - if (res < 0) - { - res = 0; - } + fixedLeft = sg.getStartRes(); + fixedRight = sg.getEndRes(); - if ((lastres == -1) || (lastres == res)) - { + 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; + } } - boolean dragRight = true; - if ((res < av.getAlignment().getWidth()) && (res < lastres)) + if(av.hasHiddenColumns ) { - dragRight = false; + 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; + } + } } - if (res != lastres) + + if (groupEditing) { - // Group editing - if (groupEditing) + Vector vseqs = sg.getSequences(true); + int g, groupSize = vseqs.size(); + SequenceI[] groupSeqs = new SequenceI[groupSize]; + for (g = 0; g < groupSeqs.length; g++) + groupSeqs[g] = (SequenceI) vseqs.elementAt(g); + + // drag to right + if (insertGap) + { + //If the user has selected the whole sequence, and is dragging to + // the right, we can still extend the alignment and selectionGroup + if( sg.getStartRes() == 0 + && sg.getEndRes() == fixedRight + && sg.getEndRes() == av.alignment.getWidth()-1 + ) + { + sg.setEndRes(av.alignment.getWidth() + startres - lastres); + fixedRight = sg.getEndRes(); + } + + // Is it valid with fixed columns?? + // Find the next gap before the end + // of the visible region boundary + boolean blank = false; + for (fixedRight = fixedRight; + fixedRight > lastres; + fixedRight--) { - SequenceGroup sg = av.getSelectionGroup(); + blank = true; - if (sg == null) + for (g = 0; g < groupSize; g++) + { + for (int j = 0; j < startres - lastres; j++) { - lastres = -1; - - return; + if (!jalview.util.Comparison.isGap( + groupSeqs[g].getCharAt(fixedRight - j))) + { + blank = false; + break; + } } + } + if (blank) + break; + } - // drag to right - if (dragRight) + if (!blank) + { + if(sg.getSize(false) == av.alignment.getHeight() ) + { + if((av.hasHiddenColumns + && startresalWidth) + alWidth = hwidth; + } + //We can still insert gaps if the selectionGroup + //contains all the sequences + sg.setEndRes(sg.getEndRes()+startres-lastres); + fixedRight = alWidth+startres-lastres; + } + else + { + endEditing(); + return; + } + } + } - if (!deleteAllowed) - { - lastres = -1; - return; - } + // drag to left + else if(!insertGap) + { + /// Are we able to delete? + // ie are all columns blank? - sg.setEndRes(sg.getEndRes() - (lastres - res)); + for (g = 0; g < groupSize; g++) + { + for (int j = startres; j < lastres; j++) + { + if (groupSeqs[g].getLength() <= j) + { + continue; } - for (int i = 0; i < sg.getSize(); i++) + if (!jalview.util.Comparison.isGap( + groupSeqs[g].getCharAt(j))) { - SequenceI s = sg.getSequenceAt(i); - int k = av.alignment.findIndex(s); - - // drag to right - if (dragRight) - { - for (int j = lastres; j < res; j++) - { - insertChar(j, k); - } - } + // Not a gap, block edit not valid + endEditing(); + return; + } + } + } + } - // drag to left - else - { - for (int j = res; j < lastres; j++) - { - if (s.getLength() > j) - { - deleteChar(res, k); - } - } - } + 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.getGapCharacter(), + true); + } } - else /////Editing a single sequence/////////// + else { - if ((res < av.getAlignment().getWidth()) && (res > lastres)) + // dragging to the left + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j > startres; j--) { - // dragging to the right - for (int j = lastres; j < res; j++) - { - insertChar(j, startseq); - } + deleteChar(startres, groupSeqs, fixedRight); } - else if ((res < av.getAlignment().getWidth()) && - (res < lastres)) + } + else + editCommand.appendEdit(EditCommand.DELETE_GAP, + groupSeqs, + startres, lastres - startres, + av.getGapCharacter(), + true); + + } + } + 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 + { + editCommand.appendEdit(EditCommand.INSERT_GAP, + new SequenceI[] + {seq}, + lastres, startres-lastres, + av.getGapCharacter(), + true); + } + } + else + { + // dragging to the left + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j > startres; j--) + { + if (!jalview.util.Comparison.isGap(seq.getCharAt(startres))) { - // dragging to the left - for (int j = lastres; j > res; j--) - { - if (jalview.util.Comparison.isGap( - av.alignment.getSequenceAt(startseq) - .getSequence().charAt(res))) - { - deleteChar(res, startseq); - } - else - { - break; - } - } + endEditing(); + break; } + deleteChar(startres, new SequenceI[]{seq}, fixedRight); + } + } + else + { + //could be a keyboard edit trying to delete none gaps + int max=0; + for(int m = startres; m0) + { + editCommand.appendEdit(EditCommand.DELETE_GAP, + new SequenceI[] + {seq}, + startres, max, + av.getGapCharacter(), + true); + } } + } } - endEdit = res; - lastres = res; + lastres = startres; seqCanvas.repaint(); } - /** - * DOCUMENT ME! - * - * @param seqstart DOCUMENT ME! - * @param seqend DOCUMENT ME! - * @param start DOCUMENT ME! - */ - public void drawChars(int seqstart, int seqend, int start) + + + void insertChar(int j, SequenceI [] seq, int fixedColumn) { - seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart, - seqend, av.getStartRes(), av.getStartSeq(), 0); - seqCanvas.repaint(); + int blankColumn = fixedColumn; + for(int s=0; s j, theres a boundary after the gap insertion + + for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) + { + if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn))) + { + //Theres a space, so break and insert the gap + break; + } + } + + if (blankColumn <= j) + { + blankColumn = fixedColumn; + endEditing(); + return; + } + } + + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + blankColumn, 1, av.getGapCharacter(), true); + + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + j, 1, av.getGapCharacter(), + true); + } - /** - * DOCUMENT ME! - * - * @param j DOCUMENT ME! - * @param seq DOCUMENT ME! - */ - public void insertChar(int j, int seq) + void deleteChar(int j, SequenceI [] seq, int fixedColumn) { - av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); - seqEditOccurred = seq; + + editCommand.appendEdit(EditCommand.DELETE_GAP, + seq, + j, 1, av.getGapCharacter(), true); + + editCommand.appendEdit(EditCommand.INSERT_GAP, + seq, + fixedColumn, 1, av.getGapCharacter(), true); } /** * DOCUMENT ME! * - * @param j DOCUMENT ME! - * @param seq DOCUMENT ME! + * @param e DOCUMENT ME! */ - public void deleteChar(int j, int seq) + public void mouseEntered(MouseEvent e) { - av.alignment.getSequenceAt(seq).deleteCharAt(j); - seqEditOccurred = seq; + if(oldSeq < 0) + oldSeq = 0; - av.alignment.getWidth(); - seqCanvas.repaint(); + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } } /** * DOCUMENT ME! * - * @param i DOCUMENT ME! + * @param e DOCUMENT ME! */ - void editOccurred(int i) + public void mouseExited(MouseEvent e) + { + if (av.getWrapAlignment()) + { + return; + } + + if (mouseDragging) + { + scrollThread = new ScrollThread(); + } + } + + public void mouseClicked(MouseEvent evt) { - if (endEdit == startEdit) + SequenceI sequence = av.alignment.getSequenceAt( findSeq(evt) ); + if(evt.getClickCount()>1) { - ap.alignFrame.historyList.pop(); - ap.alignFrame.updateEditMenuBar(); + if (av.getSelectionGroup().getSize(false) == 1 + && av.getSelectionGroup().getEndRes() + - av.getSelectionGroup().getStartRes() < 2) + av.setSelectionGroup(null); + + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), + sequence.findPosition( findRes(evt) ) + ); + + if(features!=null && features.length==1) + { + SearchResults highlight = new SearchResults(); + highlight.addResult(sequence, + features[0].getBegin(), + features[0].getEnd()); + seqCanvas.highlightSearchResults(highlight); + } + if(features!=null) + { + seqCanvas.getFeatureRenderer().amendFeatures( + new SequenceI[] + {sequence}, features, false); + + seqCanvas.highlightSearchResults(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--; + + - av.firePropertyChange("alignment", null,av.getAlignment().getSequences()); + av.setFont(new Font(font.getName(), font.getStyle(), fontSize)); + + ap.fontChanged(); + } + else*/ + { + if (e.getWheelRotation() > 0) + ap.scrollUp(false); + else + ap.scrollUp(true); + } } + /** * DOCUMENT ME! * @@ -626,13 +1280,12 @@ public class SeqPanel extends JPanel "Cannot edit annotations in wrapped view.", "Wrapped view - no edit", JOptionPane.WARNING_MESSAGE); - return; + return; } if(seq<0 || res<0) return; - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); if ((sequence == null) || (res > sequence.getLength())) @@ -656,7 +1309,7 @@ public class SeqPanel extends JPanel stretchGroup = null; } } - else if (!stretchGroup.sequences.contains(sequence) || + else if (!stretchGroup.getSequences(false).contains(sequence) || (stretchGroup.getStartRes() > res) || (stretchGroup.getEndRes() < res)) { @@ -672,57 +1325,84 @@ public class SeqPanel extends JPanel (allGroups[i].getEndRes() >= res)) { stretchGroup = allGroups[i]; - av.setSelectionGroup(stretchGroup); - break; } } } + + av.setSelectionGroup(stretchGroup); + } - 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()) + 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++) { - SliderPanel.setConservationSlider(ap, - av.getGlobalColourScheme(), "Background"); + SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i); + if (sf.links != null) + { + for (int j = 0; j < sf.links.size(); j++) + { + links.addElement(sf.links.elementAt(j)); + } + } } - if (av.getAbovePIDThreshold()) - { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); - } - } - else if (javax.swing.SwingUtilities.isRightMouseButton(evt)) - { - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null); + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links); pop.show(this, evt.getX(), evt.getY()); + return; + } - // edit the properties of existing group + if (av.cursorMode) + { + seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorY = findSeq(evt); + seqCanvas.repaint(); + return; } - if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) + if (stretchGroup == null) { + //Only if left mouse button do we want to change group sizes + + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; + + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, + av.getGlobalColourScheme(), + "Background"); + } + + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), + "Background"); + } + if ( (stretchGroup != null) && (stretchGroup.getEndRes() == res)) + { // Edit end res position of selected group changeEndRes = true; - } - else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) - { + } + else if ( (stretchGroup != null) && + (stretchGroup.getStartRes() == res)) + { // Edit end res position of selected group changeStartRes = true; + } + stretchGroup.getWidth(); } - stretchGroup.getWidth(); - seqCanvas.repaint(); } @@ -733,23 +1413,18 @@ public class SeqPanel extends JPanel */ public void doMouseReleasedDefineMode(MouseEvent evt) { - if (mouseDragging) - { - stretchGroup.recalcConservation(); - mouseDragging = false; - } - if (stretchGroup == null) { return; } + if(stretchGroup.cs!=null) { if (stretchGroup.cs instanceof ClustalxColourScheme) { - ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup. - sequences, + ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX( + stretchGroup.getSequences(true), stretchGroup.getWidth()); } @@ -757,6 +1432,7 @@ public class SeqPanel extends JPanel { SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()); + stretchGroup.recalcConservation(); } else { @@ -767,7 +1443,8 @@ public class SeqPanel extends JPanel changeEndRes = false; changeStartRes = false; stretchGroup = null; - PaintRefresher.Refresh(av.alignment); + + PaintRefresher.Refresh(this, av.getSequenceSetId()); } /** @@ -783,14 +1460,14 @@ public class SeqPanel extends JPanel if(wrappedBlock!=startWrapBlock) return; - if (stretchGroup == null) - { + if (stretchGroup == null) + { return; - } + } - if (res > av.alignment.getWidth()) + if(res>= av.alignment.getWidth()) { - res = av.alignment.getWidth() - 1; + res = av.alignment.getWidth()-1; } if (stretchGroup.getEndRes() == res) @@ -808,10 +1485,6 @@ public class SeqPanel extends JPanel { res = av.getStartRes(); } - else if (res > av.getEndRes() && !av.getWrapAlignment()) - { - res = av.getEndRes(); - } if (changeEndRes) { @@ -839,7 +1512,8 @@ public class SeqPanel extends JPanel dragDirection = -1; } - while ((y != oldSeq) && (oldSeq > 0) && (y < av.alignment.getHeight())) + + while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) { // This routine ensures we don't skip any sequences, as the // selection is quite slow. @@ -847,9 +1521,12 @@ public class SeqPanel extends JPanel oldSeq += dragDirection; + if(oldSeq<0) + break; + Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - if (stretchGroup.sequences.contains(nextSeq)) + if (stretchGroup.getSequences(false).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); } @@ -864,7 +1541,9 @@ public class SeqPanel extends JPanel } } - oldSeq = y; + if(oldSeq < 0) + oldSeq = -1; + mouseDragging = true; if (scrollThread != null) @@ -875,37 +1554,29 @@ public class SeqPanel extends JPanel seqCanvas.repaint(); } - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void doMouseEnteredDefineMode(MouseEvent e) + void scrollCanvas(MouseEvent evt) { - if (scrollThread != null) + if(evt==null) + { + if(scrollThread!=null) { - scrollThread.running = false; + scrollThread.running = false; + scrollThread = null; } - } + mouseDragging = false; + } + else + { + if (scrollThread == null) + scrollThread = new ScrollThread(); - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void doMouseExitedDefineMode(MouseEvent e) - { - if (av.getWrapAlignment()) - { - return; - } + mouseDragging = true; + scrollThread.setEvent(evt); + } - if (mouseDragging) - { - scrollThread = new ScrollThread(); - } } + // this class allows scrolling off the bottom of the visible alignment class ScrollThread extends Thread { @@ -949,17 +1620,17 @@ public class SeqPanel extends JPanel if (mouseDragging && (evt.getX() < 0)) { - running = ap.scrollRight(true); + running = ap.scrollRight(false); } else if (mouseDragging && (evt.getX() >= getWidth())) { - running = ap.scrollRight(false); + running = ap.scrollRight(true); } } try { - Thread.sleep(75); + Thread.sleep(20); } catch (Exception ex) {