X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=9ea087e9008801ec429dce5e74bad03e752d0f2d;hb=e33cdacd2ac2836504375c538574a0f1cafec7e3;hp=aa4a456dac85831044302865519675a042239fd2;hpb=07c25ef5f4631d5d385191bb01630f02fd1e06bb;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index aa4a456..9ea087e 100755 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,533 +1,1554 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 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 + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ package jalview.gui; +import jalview.datamodel.*; + +import jalview.schemes.*; + import java.awt.*; import java.awt.event.*; -import jalview.datamodel.*; + import javax.swing.*; -import jalview.schemes.*; -import jalview.analysis.*; + +import java.util.Vector; -public class SeqPanel extends JPanel +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class SeqPanel extends JPanel implements MouseListener, + MouseMotionListener, MouseWheelListener + { + /** DOCUMENT ME!! */ + public SeqCanvas seqCanvas; + + /** DOCUMENT ME!! */ + public AlignmentPanel ap; + protected int lastres; + protected int startseq; + protected AlignViewport av; + + // if character is inserted or deleted, we will need to recalculate the conservation + boolean seqEditOccurred = false; + ScrollThread scrollThread = null; + boolean mouseDragging = false; + boolean editingSeqs = false; + boolean groupEditing = false; + + ////////////////////////////////////////// + /////Everything below this is for defining the boundary of the rubberband + ////////////////////////////////////////// + int oldSeq = -1; + boolean changeEndSeq = false; + boolean changeStartSeq = false; + boolean changeEndRes = false; + boolean changeStartRes = false; + SequenceGroup stretchGroup = null; + boolean remove = false; + + Point lastMousePress; + boolean mouseWheelPressed = false; + StringBuffer keyboardNo1; + StringBuffer keyboardNo2; + + java.net.URL linkImageURL; + + /** + * 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); - public SeqCanvas seqCanvas; - public AlignmentPanel ap; + seqCanvas = new SeqCanvas(avp); + setLayout(new BorderLayout()); + add(seqCanvas, BorderLayout.CENTER); - protected int startres; - protected int lastres; - protected int endres; + ap = p; - protected int startseq; - protected int padseq; + if(!av.isDataset()) + { + addMouseMotionListener(this); + addMouseListener(this); + addMouseWheelListener(this); + } + } - protected AlignViewport av; + int startWrapBlock=-1; + int wrappedBlock=-1; + int findRes(MouseEvent evt) + { + int res = 0; + int x = evt.getX(); - // if character is inserted or deleted, we will need to recalculate the conservation - int seqEditOccurred = -1; + if (av.wrapAlignment) + { - public SeqPanel(AlignViewport avp, AlignmentPanel p) { - this.av = avp; + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; - seqCanvas = new SeqCanvas(avp); - setLayout(new BorderLayout()); - add(seqCanvas, BorderLayout.CENTER); + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); - ap = p; + int y = evt.getY(); + y -= hgap; + x -= seqCanvas.LABEL_WEST; - addMouseMotionListener( new MouseMotionAdapter() - { - public void mouseMoved(MouseEvent evt) - { - if(av.getWrapAlignment()) - return; - doMouseMoved(evt); } - public void mouseDragged(MouseEvent evt) - { - if(av.getWrapAlignment()) - return; - if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) - doMouseDragged(evt); - else - doMouseDraggedDefineMode(evt); - } - }); + int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); + + wrappedBlock = y / cHeight; + wrappedBlock += av.getStartRes() / cwidth; - addMouseListener( new MouseAdapter() + res = wrappedBlock * cwidth + x / av.getCharWidth(); + + } + else { - public void mouseReleased(MouseEvent evt) - { - if(av.getWrapAlignment()) - return; - if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) - doMouseReleased(evt); - else - doMouseReleasedDefineMode(evt); - } - public void mousePressed(MouseEvent evt) - { - if(av.getWrapAlignment()) - return; - if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) - doMousePressed(evt); - else - doMousePressedDefineMode(evt); - } + res = (x / av.getCharWidth()) + av.getStartRes(); + } - }); - repaint(); - } + if(av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); + return res; - public void doMouseReleased(MouseEvent evt) { + } - int x = evt.getX(); - int res = x/av.getCharWidth() + av.getStartRes(); + int findSeq(MouseEvent evt) + { - endres = res; + int seq = 0; + int y = evt.getY(); - startseq = -1; - startres = -1; - lastres = -1; - if(seqEditOccurred>-1) - updateConservation(seqEditOccurred); + if (av.wrapAlignment) + { + int hgap = av.charHeight; + if (av.scaleAboveWrapped) + hgap += av.charHeight; - seqEditOccurred = -1; + int cHeight = av.getAlignment().getHeight() * av.charHeight + + hgap + seqCanvas.getAnnotationHeight(); - ap.RefreshPanels(); - repaint(); + y -= hgap; - } + seq = ( (y % cHeight) / av.getCharHeight()); + } + else + { + seq = (y / av.getCharHeight()) + av.getStartSeq(); + } - public void doMousePressed(MouseEvent evt) { - ap.alignFrame.addHistoryItem("sequence edit"); - int seq; - int res; + return seq; + } - int x = evt.getX(); - int y = evt.getY(); + Vector getAllFeaturesAtRes(SequenceI seq, int res) + { + Vector allFeatures = new Vector(); + int index = 0; + if(seq.getSequenceFeatures()!=null && av.featuresDisplayed!=null) + { + while (index < seq.getSequenceFeatures().length) + { + SequenceFeature sf = seq.getSequenceFeatures()[index]; + if (sf.getBegin() <= res && + sf.getEnd() >= res) + { + if (av.featuresDisplayed.containsKey(sf.getType())) + { + allFeatures.addElement(sf); + } + } + index++; + } + } + return allFeatures; + } - res = x/av.getCharWidth() + av.getStartRes(); - seq = y/av.getCharHeight() + av.getStartSeq(); + void endEditing() + { + startseq = -1; + lastres = -1; + seqEditOccurred = false; + editingSeqs = false; + groupEditing = false; + keyboardNo1 = null; + keyboardNo2 = null; + } - if (seq < av.getAlignment().getHeight() && - res < av.getAlignment().getSequenceAt(seq).getLength()) + void setCursorRow() { - //char resstr = align.getSequenceAt(seq).getSequence().charAt(res); - // Find the residue's position in the sequence (res is the position - // in the alignment + seqCanvas.cursorY = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } - startseq = seq; + void setCursorColumn() + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1)-1; + scrollToVisible(); + } - if (startseq == (av.getAlignment().getHeight() - 1)) - padseq = 1; + void setCursorRowAndColumn() + { + if(keyboardNo2==null) + { + keyboardNo2 = new StringBuffer(); + } else - padseq = 1; + { + seqCanvas.cursorX = getKeyboardNo(keyboardNo1) - 1; + seqCanvas.cursorY = getKeyboardNo(keyboardNo2) - 1; + scrollToVisible(); + } + } - startres = res; - lastres = res; + void setCursorPosition() + { + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + seqCanvas.cursorX = sequence.findIndex( + getKeyboardNo(keyboardNo1)-1 + ); + scrollToVisible(); } - else + + void moveCursor(int dx, int dy) { - startseq = -1; - startres = -1; - lastres = -1; + seqCanvas.cursorX += dx; + seqCanvas.cursorY += dy; + scrollToVisible(); } - return; - } - - public void doMouseMoved(MouseEvent evt) - { - int res=0, seq=0; - int x = evt.getX(); - int y = evt.getY(); - if(av.wrapAlignment) + void scrollToVisible() { - y -= 2*av.charHeight; - int chunkHeight = (av.getAlignment().getHeight()+2)*av.charHeight; + 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; - res = (int)((y/chunkHeight)*(getWidth()/av.charWidth)) + x/av.getCharWidth() + av.getStartRes(); - y %= chunkHeight; - seq = y / av.getCharHeight() + av.getStartSeq(); + 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); - // chunkHeight = (da.getHeight() + 2)*charHeight; - // startx += chunkWidth; + seqCanvas.repaint(); } - else + + void setSelectionAreaAtCursor(boolean topLeft) { - res = x / av.getCharWidth() + av.getStartRes(); - seq = y / av.getCharHeight() + av.getStartSeq(); - } + SequenceI sequence = + (Sequence) av.getAlignment().getSequenceAt(seqCanvas.cursorY); + if(av.getSelectionGroup()!=null) + { + SequenceGroup sg = av.selectionGroup; + //Find the top and bottom of this group + int min = av.alignment.getHeight(), max = 0; + for(int i=0; i max) + max = index; + if(index < min) + min = index; + } - if(seq>=av.getAlignment().getHeight()) - return; + max ++; - Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ; - String aa = ""; - if(obj!=null) - aa = obj.toString(); + if(topLeft) + { + sg.setStartRes(seqCanvas.cursorX); + if(sg.getEndRes()seqCanvas.cursorX) + sg.setStartRes(seqCanvas.cursorX); - ap.alignFrame.statusBar.setText(text.toString()); + 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); + } + } + } - public void doMouseDragged(MouseEvent evt) { - // If we're dragging we're editing + if (av.getSelectionGroup() == null) + { + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(seqCanvas.cursorX); + sg.setEndRes(seqCanvas.cursorX); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + } - int x = evt.getX(); - int res = x/av.getCharWidth() + av.getStartRes(); - if (res < 0) - res = 0; + ap.repaint(); + } - if (res != lastres) + void insertGapAtCursor(boolean group) { - // Group editing - if (evt.isAltDown() || evt.isControlDown()) - { - SequenceGroup sg = av.getAlignment().findGroup(startseq); - if (sg != null) - { - boolean deleteAllowed = false; - if (res < av.getAlignment().getWidth() && res < lastres) - { - /// Are we able to delete? - boolean allGaps = true; - for (int i = 0; i < sg.getSize(); i++) - { - SequenceI s = sg.getSequenceAt(i); - for (int j = lastres-1; j >= res && allGaps; j--) - { - if (!jalview.util.Comparison.isGap(s.getSequence().charAt(j))) - { - res = j + 1; - allGaps = false; - } - } - - if(!deleteAllowed && allGaps) - deleteAllowed = true; - } - } - - // drag to right - if (res < av.getAlignment().getWidth() && res > lastres) - sg.setEndRes(sg.getEndRes() + 1); + 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(); + } - // drag to left - else if (deleteAllowed && res < av.getAlignment().getWidth() && - res < lastres) - sg.setEndRes(sg.getEndRes() - 1); + void deleteGapAtCursor(boolean group) + { + ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", + av.alignment, HistoryItem.EDIT)); + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX+getKeyboardNo(keyboardNo1); + editSequence(false, seqCanvas.cursorX); + editOccurred(); + } + void numberPressed(char value) + { + if(keyboardNo1==null) + keyboardNo1 = new StringBuffer(); + if(keyboardNo2!=null) + keyboardNo2.append(value); + else + keyboardNo1.append(value); + } + int getKeyboardNo(StringBuffer kb) + { + if(kb==null) + return 1; + else + return Integer.parseInt(kb.toString()); + } - for (int i = 0; i < sg.getSize(); i++) - { - SequenceI s = sg.getSequenceAt(i); - int k = av.alignment.findIndex(s); - // drag to right - if (res < av.getAlignment().getWidth() && res > lastres) - for (int j = lastres; j < res; j++) - insertChar(j, k); + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseReleased(MouseEvent evt) + { + mouseDragging = false; + mouseWheelPressed = false; - // drag to left - else if (deleteAllowed && res < av.getAlignment().getWidth() && res < lastres) - { - for (int j = res; j < lastres; j++) - { - deleteChar(j, k); - startres = res; - } - } - } - } - } - else /////Editing a single sequence/////////// - { - if (res < av.getAlignment().getWidth() && res > lastres) - { - // dragging to the right - for (int j = lastres; j < res; j++) - insertChar(j, startseq); - } - else if (res < av.getAlignment().getWidth() && res < lastres) - { - // dragging to the left - for (int j = res; j < lastres; j++) - { - deleteChar(j, startseq); - startres = res; - } - } + if (!editingSeqs) + { + doMouseReleasedDefineMode(evt); + return; + } - } + editOccurred(); + ap.repaint(); } - lastres = res; - repaint(); - } - public void drawChars(int seqstart, int seqend, int start) { - seqCanvas.drawPanel(seqCanvas.gg, start,av.getEndRes(),seqstart,seqend,av.getStartRes(),av.getStartSeq(),0); - repaint(); - } - public void insertChar(int j, int seq) - { - av.alignment.getSequenceAt(seq).insertCharAt(j, av.getGapCharacter()); - seqEditOccurred=seq; - } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mousePressed(MouseEvent evt) + { + lastMousePress = evt.getPoint(); - public void deleteChar(int j, int seq) - { + 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; + } - if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j))) - av.alignment.getSequenceAt(seq).deleteCharAt(j); - av.alignment.getWidth(); - repaint(); - seqEditOccurred=seq; - } + int seq = findSeq(evt); + int res = findRes(evt); - void updateConservation(int i) - { - /* Alignment al = (Alignment) av.getAlignment(); - SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i)); - if(sg==null || !(sg.cs instanceof ConservationColourScheme)) - return; + if(seq<0 || res<0) + return; - Conservation c = sg.getConservation(); + ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence", + av.alignment, HistoryItem.EDIT)); - c = new Conservation("All", al.cons, - ResidueProperties.propHash, 3, sg.sequences, 0, - al.getWidth()); - c.calculate(); - c.verdict(false, 100); - sg.setConservation(c); - ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; - ccs.conserve = c;*/ - } + if ((seq < av.getAlignment().getHeight()) && + (res < av.getAlignment().getSequenceAt(seq).getLength())) + { + startseq = seq; + lastres = res; + } + else + { + startseq = -1; + lastres = -1; + } -////////////////////////////////////////// -/////Everything below this is for defining the boundary of the rubberband -////////////////////////////////////////// - int oldSeq = -1; - public void doMousePressedDefineMode(MouseEvent evt) - { - int res = evt.getX()/av.getCharWidth() + av.getStartRes(); - int seq = evt.getY()/av.getCharHeight() + av.getStartSeq(); - oldSeq = seq; + return; + } - stretchGroup = av.getRubberbandGroup(); + /** + * 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(stretchGroup == null) - { - stretchGroup = av.alignment.findGroup( (Sequence) av.getAlignment(). - getSequenceAt(seq)); - av.setRubberbandGroup( stretchGroup ); - } + int res = findRes(evt); + int seq = findSeq(evt); - else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq)) - || stretchGroup.getStartRes()>res - || stretchGroup.getEndRes()= av.getAlignment().getHeight()) + return; - if (allGroups != null) - for (int i = 0; i < allGroups.length; i++) - if (allGroups[i].getStartRes() <= res && - allGroups[i].getEndRes() >= res) - { - stretchGroup = allGroups[i]; - av.setRubberbandGroup(stretchGroup); - break; - } - } + SequenceI sequence = av.getAlignment().getSequenceAt(seq); - if(stretchGroup==null) - { - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) ); - av.setRubberbandGroup( sg ); - stretchGroup = sg; + if (res > sequence.getLength()) + { + return; + } - if(av.getConservationSelected()) - Desktop.setConservationSliderSource(ap, av.getGlobalColourScheme(), "Background"); - else if(av.getGlobalColourScheme()!=null && av.getGlobalColourScheme().canThreshold()) + if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence) { - ResidueColourScheme rcs = (ResidueColourScheme) av.getGlobalColourScheme(); - int threshold = rcs.getThreshold(); - if (threshold > 0) - Desktop.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background"); + seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res)); } - } - else if( javax.swing.SwingUtilities.isRightMouseButton(evt)) - { - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null); - pop.show(this, evt.getX(), evt.getY()); + setStatusMessage(sequence, res, seq); - // edit the properties of existing group - } + // use aa to see if the mouse pointer is on a + if (av.showSequenceFeatures) + { + SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures(); + if(features!=null) + { + StringBuffer sbuffer = new StringBuffer(""); + StringBuffer seqSpecific = new StringBuffer(); - if(stretchGroup!=null && stretchGroup.getEndRes()==res) - // Edit end res position of selected group - changeEndRes = true; + for (int i = 0; i < features.length; i++) + { - else if(stretchGroup!=null && stretchGroup.getStartRes()==res) - // Edit end res position of selected group - changeStartRes = true; + if ( (features[i].getBegin() <= sequence.findPosition(res)) && + (features[i].getEnd() >= sequence.findPosition(res))) + { + if(av.featuresDisplayed==null + || !av.featuresDisplayed.containsKey(features[i].getType())) + continue; - seqCanvas.paintFlag = true; - repaint(); + 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()); + if (features[i].links != null) + sbuffer.append(" "); + } + } + else + { + if (sbuffer.length() > 6) + sbuffer.append("
"); + + sbuffer.append(features[i].getType() + " " + + features[i].begin); + if (features[i].begin != features[i].end) + sbuffer.append(" " + features[i].end); + + if (features[i].getDescription() != null + && !features[i].description.equals(features[i].getType())) + sbuffer.append("; " + features[i].getDescription()); + + if (features[i].getValue("status") != null) + { + sbuffer.append("; (" + features[i].getValue("status") + ")"); + } + if (features[i].links != null) + sbuffer.append(" "); - } + } + } + else if(features[i].begin==0 && features[i].end==0) + { + // seqSpecific.append(features[i].featureGroup+": " + // + features[i].getType()+" " + // +features[i].getDescription()+"
"); - boolean changeEndSeq = false; - boolean changeStartSeq = false; - boolean changeEndRes = false; - boolean changeStartRes = false; - SequenceGroup stretchGroup = null; + } + } - public void doMouseReleasedDefineMode(MouseEvent evt) - { + if(seqSpecific.length()>0) + seqSpecific.setLength(seqSpecific.length()-4); - if(stretchGroup.cs instanceof ClustalxColourScheme) - { - stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth()); - seqCanvas.paintFlag = true; - repaint(); + sbuffer.append(seqSpecific); + sbuffer.append(""); + if(sbuffer.length()==13) // + setToolTipText(""); + else + setToolTipText(sbuffer.toString()); + } + else + setToolTipText(""); + } } - else if(stretchGroup.cs instanceof ConservationColourScheme) + void setStatusMessage(SequenceI sequence, int res, int seq) { - ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs; - - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, stretchGroup.sequences, 0, - av.alignment.getWidth() ); + StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " + + sequence.getName()); - c.calculate(); - c.verdict(false, 100); - ccs = new ConservationColourScheme(c, ccs.cs); - - stretchGroup.cs = ccs; + 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) + { - Desktop.setConservationSliderSource(ap, stretchGroup.cs, stretchGroup.getName()) ; + if (obj != "") + { + text.append(obj + " (" + sequence.findPosition(res) + + ")"); + } + } + ap.alignFrame.statusBar.setText(text.toString()); - seqCanvas.paintFlag = true; - repaint(); } - else + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseDragged(MouseEvent evt) { - if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold()) + if (mouseWheelPressed) { - ResidueColourScheme rcs = (ResidueColourScheme) stretchGroup.cs; - int threshold = rcs.getThreshold(); - if(threshold>0) - Desktop.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName()); - } + 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; - changeEndRes = false; - changeStartRes = false; - stretchGroup = null; - } + 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; - boolean remove = false; - public void doMouseDraggedDefineMode(MouseEvent evt) - { - int res = evt.getX()/av.getCharWidth() + av.getStartRes(); - int y = evt.getY()/av.getCharHeight() + av.getStartSeq(); + lastMousePress = evt.getPoint(); + return; + } - if(stretchGroup.getEndRes()==res) - // Edit end res position of selected group - changeEndRes = true; + if (!editingSeqs) + { + doMouseDraggedDefineMode(evt); + return; + } - else if(stretchGroup.getStartRes()==res) - // Edit start res position of selected group - changeStartRes = true; + int res = findRes(evt); + if (res < 0) + { + res = 0; + } - if(resav.getEndRes()) - res = av.getEndRes(); + if ((lastres == -1) || (lastres == res)) + { + return; + } - if(changeEndRes) - { - if(res>stretchGroup.getStartRes()-1) - stretchGroup.setEndRes( res ); - } - else if(changeStartRes) - { - if(res oldSeq) - dragDirection = 1; - else if (y < oldSeq) - dragDirection = -1; + } - while (y != oldSeq) + synchronized void editSequence(boolean insertGap, int startres) { - // This routine ensures we don't skip any sequences, as the - // selection is quite slow. - Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); + int fixedLeft = -1; + int fixedRight = -1; + boolean fixedColumns = false; + SequenceGroup sg = av.getSelectionGroup(); - oldSeq += dragDirection; - Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); - if (stretchGroup.sequences.contains(nextSeq)) - { - stretchGroup.deleteSequence(seq); - stretchGroup.deleteSequence(nextSeq); - } - else - { - stretchGroup.addSequence(seq); - stretchGroup.addSequence(nextSeq); - } - } - oldSeq = y; + if (!groupEditing && av.hasHiddenRows) + { + if (av.alignment.getSequenceAt(startseq).getHiddenSequences() != null) + { + groupEditing = true; + } + } - seqCanvas.paintFlag = true; - repaint(); - } + //No group, but the sequence may represent a group + if (groupEditing + && sg == null + && av.alignment.getSequenceAt(startseq).getHiddenSequences() == null) + { + groupEditing = false; + } + SequenceI seq = av.alignment.getSequenceAt(startseq); + StringBuffer message = new StringBuffer(); + if (groupEditing) + message.append("Edit group:"); + else + message.append("Edit sequence: "+seq.getName()); -} + if(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(true).contains(seq))) + { + fixedColumns = true; + //sg might be null as the user may only see 1 sequence, + //but the sequence represents a group + if (sg == null) + { + sg = new SequenceGroup(null, null, false, false, false, 0, + av.alignment.getWidth()-1); + sg.addSequence(av.alignment.getSequenceAt(startseq), false); + } + + fixedLeft = sg.getStartRes(); + fixedRight = sg.getEndRes(); + + if ( (startres < fixedLeft && lastres >= fixedLeft) + || (startres >= fixedLeft && lastres < fixedLeft) + || (startres > fixedRight && lastres <=fixedRight) + || (startres <= fixedRight && lastres > fixedRight)) + { + endEditing(); + return; + } + + if (fixedLeft > startres) + { + fixedRight = fixedLeft - 1; + fixedLeft = 0; + } + else if (fixedRight < startres) + { + fixedLeft = fixedRight; + fixedRight = -1; + } + } + + + if(av.hasHiddenColumns ) + { + fixedColumns = true; + int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); + int y2 = av.getColumnSelection().getHiddenBoundaryRight(startres); + + if ( (insertGap && startres > y1 && lastres < y1) + || (!insertGap && startres < y2 && lastres > y2)) + { + endEditing(); + return; + } + + //System.out.print(y1+" "+y2+" "+fixedLeft+" "+fixedRight+"~~"); + //Selection spans a hidden region + if(fixedLefty2 || fixedRight==-1)) + { + if(startres>=y2) + { + fixedLeft = y2; + } + else + { + fixedRight = y2 - 1; + } + } + } + + + if (groupEditing) + { + // drag to right + if (insertGap) + { + //If the user has selected the whole sequence, and is dragging to + // the right, we can still extend the alignment and selectionGroup + if( sg.getStartRes() == 0 + && sg.getEndRes() == fixedRight + && sg.getEndRes() == av.alignment.getWidth()-1 + ) + { + sg.setEndRes(av.alignment.getWidth() + startres - lastres); + fixedRight = sg.getEndRes(); + } + + // Is it valid with fixed columns?? + // Find the next gap before the end + // of the visible region boundary + boolean blank = false; + for (fixedRight = fixedRight; + fixedRight > lastres; + fixedRight--) + { + blank = true; + for (int s = 0; s < sg.getSize(true); s++) + { + seq = (SequenceI)sg.getSequences(true).elementAt(s); + for (int j = 0; j < startres - lastres; j++) + { + if (!jalview.util.Comparison.isGap( + seq.getCharAt(fixedRight - j))) + { + blank = false; + break; + } + } + } + if (blank) + break; + } + + 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; + } + } + } + + + // drag to left + else if(!insertGap) + { + /// Are we able to delete? + // ie are all columns blank? + + for (int s = 0; s < sg.getSize(true); s++) + { + seq = (SequenceI)sg.getSequences(true).elementAt(s); + + for (int j = startres; j < lastres; j++) + { + if (seq.getSequence().length() <= j) + { + continue; + } + + if (!jalview.util.Comparison.isGap( + seq.getSequence().charAt(j))) + { + // Not a gap, block edit not valid + endEditing(); + return; + } + } + } + } + + + for (int i = 0; i < sg.getSize(true); i++) + { + seq = (SequenceI) sg.getSequences(true).elementAt(i); + + 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 + 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); + } + } + } + } + + lastres = startres; + seqCanvas.repaint(); + } + + + /** + * DOCUMENT ME! + * + * @param j DOCUMENT ME! + * @param seq DOCUMENT ME! + */ + void insertChar(int j, SequenceI seq) + { + seq.insertCharAt(j, av.getGapCharacter()); + seqEditOccurred = true; + } + + void insertChar(int j, SequenceI seq, int fixedColumn) + { + //Find the next gap before the end of the visible region boundary + //If lastCol > j, theres a boundary after the gap insertion + int blankColumn = fixedColumn; + for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) + { + if (jalview.util.Comparison.isGap(seq.getCharAt(blankColumn))) + { + //Theres a space, so break and insert the gap + break; + } + } + + if (blankColumn <= j) + { + System.out.println("END HERE "+seq.getName()+" "+seq.getLength()+" "+j+" " + +blankColumn+" "+fixedColumn); + blankColumn = fixedColumn; + endEditing(); + return; + } + + if (!jalview.util.Comparison.isGap(seq.getCharAt(blankColumn))) + { + //Just Checking + System.out.println("Tried removing residue (INSERT)"+seq.getCharAt(fixedColumn)); + return; + } + + seq.deleteCharAt(blankColumn); + seq.insertCharAt(j, av.getGapCharacter()); + seqEditOccurred = true; + } + + void deleteChar(int j, SequenceI seq, int fixedColumn) + { + if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) + { + ap.alignFrame.statusBar.setText( + "End editing: Tried removing residue " + seq.getCharAt(j)); + return; + } + + seq.deleteCharAt(j); + seq.insertCharAt(fixedColumn, av.getGapCharacter()); + seqEditOccurred = true; + } + + /** + * DOCUMENT ME! + * + * @param j DOCUMENT ME! + * @param seq DOCUMENT ME! + */ + void deleteChar(int j, SequenceI seq) + { + if (!jalview.util.Comparison.isGap(seq.getCharAt(j))) + { + ap.alignFrame.statusBar.setText( + "End editing: Tried removing residue " + seq.getCharAt(j)); + return; + } + + seq.deleteCharAt(j); + seqEditOccurred = true; + seqCanvas.repaint(); + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void mouseEntered(MouseEvent e) + { + if(oldSeq < 0) + oldSeq = 0; + + if (scrollThread != null) + { + scrollThread.running = false; + scrollThread = null; + } + } + + /** + * 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) + {} + + 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.setFont(new Font(font.getName(), font.getStyle(), fontSize)); + + ap.fontChanged(); + } + else*/ + { + if (e.getWheelRotation() > 0) + ap.scrollUp(false); + else + ap.scrollUp(true); + } + + } + + + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + */ + void editOccurred() + { + if (!seqEditOccurred) + { + ap.alignFrame.historyList.pop(); + ap.alignFrame.updateEditMenuBar(); + } + + endEditing(); + + av.firePropertyChange("alignment", null,av.getAlignment().getSequences()); + + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMousePressedDefineMode(MouseEvent evt) + { + int res = findRes(evt); + int seq = findSeq(evt); + oldSeq = seq; + + startWrapBlock=wrappedBlock; + + if(av.wrapAlignment && seq>av.alignment.getHeight()) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Cannot edit annotations in wrapped view.", + "Wrapped view - no edit", + JOptionPane.WARNING_MESSAGE); + return; + } + + if(seq<0 || res<0) + return; + + SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); + + if ((sequence == null) || (res > sequence.getLength())) + { + return; + } + + stretchGroup = av.getSelectionGroup(); + + if (stretchGroup == null) + { + stretchGroup = av.alignment.findGroup(sequence); + + if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) && + (res < stretchGroup.getEndRes())) + { + av.setSelectionGroup(stretchGroup); + } + else + { + stretchGroup = null; + } + } + else if (!stretchGroup.getSequences(false).contains(sequence) || + (stretchGroup.getStartRes() > res) || + (stretchGroup.getEndRes() < res)) + { + stretchGroup = null; + + SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); + + if (allGroups != null) + { + for (int i = 0; i < allGroups.length; i++) + { + if ((allGroups[i].getStartRes() <= res) && + (allGroups[i].getEndRes() >= res)) + { + stretchGroup = allGroups[i]; + break; + } + } + } + + av.setSelectionGroup(stretchGroup); + + } + + if (av.cursorMode) + { + seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorY = findSeq(evt); + seqCanvas.repaint(); + return; + } + + + if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + { + Vector allFeatures = getAllFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); + Vector links = new Vector(); + for (int i = 0; i < allFeatures.size(); i++) + { + SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i); + if (sf.links != null) + { + for (int j = 0; j < sf.links.size(); j++) + { + links.addElement(sf.links.elementAt(j)); + } + } + } + + jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links); + pop.show(this, evt.getX(), evt.getY()); + + } + else 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)) + { + // Edit end res position of selected group + changeStartRes = true; + } + stretchGroup.getWidth(); + } + + seqCanvas.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseReleasedDefineMode(MouseEvent evt) + { + if (stretchGroup == null) + { + return; + } + + + if(stretchGroup.cs!=null) + { + if (stretchGroup.cs instanceof ClustalxColourScheme) + { + ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX( + stretchGroup.getSequences(true), + stretchGroup.getWidth()); + } + + 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); + } + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void doMouseDraggedDefineMode(MouseEvent evt) + { + int res = findRes(evt); + int y = findSeq(evt); + + if(wrappedBlock!=startWrapBlock) + return; + + if (stretchGroup == null) + { + return; + } + + + if(y > av.alignment.getHeight()) + { + y = av.alignment.getHeight() -1; + } + if(res> av.alignment.getWidth()) + { + res = av.alignment.getWidth()-1; + } + + if (stretchGroup.getEndRes() == res) + { + // Edit end res position of selected group + changeEndRes = true; + } + else if (stretchGroup.getStartRes() == res) + { + // Edit start res position of selected group + changeStartRes = true; + } + + if (res < av.getStartRes()) + { + res = av.getStartRes(); + } + + if (changeEndRes) + { + if (res > (stretchGroup.getStartRes() - 1)) + { + stretchGroup.setEndRes(res); + } + } + else if (changeStartRes) + { + if (res < (stretchGroup.getEndRes() + 1)) + { + stretchGroup.setStartRes(res); + } + } + + int dragDirection = 0; + + if (y > oldSeq) + { + dragDirection = 1; + } + else if (y < oldSeq) + { + dragDirection = -1; + } + + + while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) + { + // This routine ensures we don't skip any sequences, as the + // selection is quite slow. + Sequence seq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); + + oldSeq += dragDirection; + + if(oldSeq<0) + break; + + Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq); + + if (stretchGroup.getSequences(false).contains(nextSeq)) + { + stretchGroup.deleteSequence(seq, false); + } + else + { + if (seq != null) + { + stretchGroup.addSequence(seq, false); + } + + stretchGroup.addSequence(nextSeq, false); + } + } + + if(oldSeq < 0) + oldSeq = -1; + + mouseDragging = true; + + if (scrollThread != null) + { + scrollThread.setEvent(evt); + } + + seqCanvas.repaint(); + } + + void scrollCanvas(MouseEvent evt) + { + if(evt==null) + { + if(scrollThread!=null) + { + scrollThread.running = false; + scrollThread = null; + } + mouseDragging = false; + } + else + { + if (scrollThread == null) + scrollThread = new ScrollThread(); + + mouseDragging = true; + scrollThread.setEvent(evt); + } + + } + + + // this class allows scrolling off the bottom of the visible alignment + class ScrollThread extends Thread + { + MouseEvent evt; + boolean running = false; + + public ScrollThread() + { + start(); + } + + public void setEvent(MouseEvent e) + { + evt = e; + } + + public void stopScrolling() + { + running = false; + } + + public void run() + { + 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) + { + } + } + } + } +}