X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=cdaa5b949c903dcdc41581c30a1563f9d0afc953;hb=af563e083b2a94e50f23d317f260fb734c52c266;hp=bdfcef466942d8965fa6b621416cf999f9745c77;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java old mode 100755 new mode 100644 index bdfcef4..cdaa5b9 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,27 +1,28 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview 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 + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . */ package jalview.gui; import java.util.*; +import java.util.List; import java.awt.*; import java.awt.event.*; + import javax.swing.*; import jalview.commands.*; @@ -31,12 +32,13 @@ import jalview.structure.*; /** * DOCUMENT ME! - * + * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.130 $ */ public class SeqPanel extends JPanel implements MouseListener, - MouseMotionListener, MouseWheelListener, SequenceListener + MouseMotionListener, MouseWheelListener, SequenceListener, + SelectionListener { /** DOCUMENT ME!! */ @@ -96,11 +98,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * Creates a new SeqPanel object. - * + * * @param avp - * DOCUMENT ME! + * DOCUMENT ME! * @param p - * DOCUMENT ME! + * DOCUMENT ME! */ public SeqPanel(AlignViewport av, AlignmentPanel ap) { @@ -122,8 +124,9 @@ public class SeqPanel extends JPanel implements MouseListener, addMouseMotionListener(this); addMouseListener(this); addMouseWheelListener(this); - ssm = StructureSelectionManager.getStructureSelectionManager(); + ssm = StructureSelectionManager.getStructureSelectionManager(Desktop.instance); ssm.addStructureViewerListener(this); + ssm.addSelectionListener(this); } } @@ -166,10 +169,15 @@ public class SeqPanel extends JPanel implements MouseListener, } else { + if (x>seqCanvas.getWidth()+seqCanvas.getWidth()) + { + // make sure we calculate relative to visible alignment, rather than right-hand gutter + x = seqCanvas.getX()+seqCanvas.getWidth(); + } res = (x / av.getCharWidth()) + av.getStartRes(); } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { res = av.getColumnSelection().adjustForHiddenColumns(res); } @@ -196,13 +204,13 @@ public class SeqPanel extends JPanel implements MouseListener, y -= hgap; - seq = Math.min((y % cHeight) / av.getCharHeight(), av.alignment - .getHeight() - 1); + seq = Math.min((y % cHeight) / av.getCharHeight(), + av.getAlignment().getHeight() - 1); } else { seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), - av.alignment.getHeight() - 1); + av.getAlignment().getHeight() - 1); } return seq; @@ -290,7 +298,7 @@ public class SeqPanel extends JPanel implements MouseListener, void setCursorPosition() { - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt( + SequenceI sequence = av.getAlignment().getSequenceAt( seqCanvas.cursorY); seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1() - 1); @@ -301,19 +309,19 @@ public class SeqPanel extends JPanel implements MouseListener, { seqCanvas.cursorX += dx; seqCanvas.cursorY += dy; - if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX)) + if (av.hasHiddenColumns() && !av.getColumnSelection().isVisible(seqCanvas.cursorX)) { int original = seqCanvas.cursorX - dx; - int maxWidth = av.alignment.getWidth(); + int maxWidth = av.getAlignment().getWidth(); - while (!av.colSel.isVisible(seqCanvas.cursorX) + while (!av.getColumnSelection().isVisible(seqCanvas.cursorX) && seqCanvas.cursorX < maxWidth && seqCanvas.cursorX > 0) { seqCanvas.cursorX += dx; } if (seqCanvas.cursorX >= maxWidth - || !av.colSel.isVisible(seqCanvas.cursorX)) + || !av.getColumnSelection().isVisible(seqCanvas.cursorX)) { seqCanvas.cursorX = original; } @@ -328,18 +336,18 @@ public class SeqPanel extends JPanel implements MouseListener, { seqCanvas.cursorX = 0; } - else if (seqCanvas.cursorX > av.alignment.getWidth() - 1) + else if (seqCanvas.cursorX > av.getAlignment().getWidth() - 1) { - seqCanvas.cursorX = av.alignment.getWidth() - 1; + seqCanvas.cursorX = av.getAlignment().getWidth() - 1; } if (seqCanvas.cursorY < 0) { seqCanvas.cursorY = 0; } - else if (seqCanvas.cursorY > av.alignment.getHeight() - 1) + else if (seqCanvas.cursorY > av.getAlignment().getHeight() - 1) { - seqCanvas.cursorY = av.alignment.getHeight() - 1; + seqCanvas.cursorY = av.getAlignment().getHeight() - 1; } endEditing(); @@ -359,7 +367,7 @@ public class SeqPanel extends JPanel implements MouseListener, } if (!av.wrapAlignment) { - while (seqCanvas.cursorX < av.colSel + while (seqCanvas.cursorX < av.getColumnSelection() .adjustForHiddenColumns(av.startRes)) { if (!ap.scrollRight(false)) @@ -367,7 +375,7 @@ public class SeqPanel extends JPanel implements MouseListener, break; } } - while (seqCanvas.cursorX > av.colSel + while (seqCanvas.cursorX > av.getColumnSelection() .adjustForHiddenColumns(av.endRes)) { if (!ap.scrollRight(true)) @@ -377,7 +385,7 @@ public class SeqPanel extends JPanel implements MouseListener, } } } - setStatusMessage(av.alignment.getSequenceAt(seqCanvas.cursorY), + setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); seqCanvas.repaint(); @@ -385,17 +393,17 @@ public class SeqPanel extends JPanel implements MouseListener, void setSelectionAreaAtCursor(boolean topLeft) { - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt( + SequenceI sequence = av.getAlignment().getSequenceAt( seqCanvas.cursorY); if (av.getSelectionGroup() != null) { - SequenceGroup sg = av.selectionGroup; + SequenceGroup sg = av.getSelectionGroup(); // Find the top and bottom of this group - int min = av.alignment.getHeight(), max = 0; + int min = av.getAlignment().getHeight(), max = 0; for (int i = 0; i < sg.getSize(); i++) { - int index = av.alignment.findIndex(sg.getSequenceAt(i)); + int index = av.getAlignment().findIndex(sg.getSequenceAt(i)); if (index > max) { max = index; @@ -440,7 +448,7 @@ public class SeqPanel extends JPanel implements MouseListener, sg.getSequences(null).clear(); for (int i = min; i < max; i++) { - sg.addSequence(av.alignment.getSequenceAt(i), false); + sg.addSequence(av.getAlignment().getSequenceAt(i), false); } } } @@ -455,6 +463,7 @@ public class SeqPanel extends JPanel implements MouseListener, } ap.paintAlignment(false); + av.sendSelection(); } void insertGapAtCursor(boolean group) @@ -462,7 +471,7 @@ public class SeqPanel extends JPanel implements MouseListener, groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; - editSequence(true, seqCanvas.cursorX + getKeyboardNo1()); + editSequence(true, false, seqCanvas.cursorX + getKeyboardNo1()); endEditing(); } @@ -471,10 +480,18 @@ public class SeqPanel extends JPanel implements MouseListener, groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX + getKeyboardNo1(); - editSequence(false, seqCanvas.cursorX); + editSequence(false, false, seqCanvas.cursorX); endEditing(); } + void insertNucAtCursor(boolean group,String nuc){ + groupEditing = group; + startseq = seqCanvas.cursorY; + lastres = seqCanvas.cursorX; + editSequence(false, true, seqCanvas.cursorX + getKeyboardNo1()); + endEditing(); + } + void numberPressed(char value) { if (keyboardNo1 == null) @@ -518,10 +535,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent evt) { mouseDragging = false; @@ -538,10 +556,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent evt) { lastMousePress = evt.getPoint(); @@ -591,6 +610,7 @@ public class SeqPanel extends JPanel implements MouseListener, String lastMessage; + @Override public void mouseOverSequence(SequenceI sequence, int index, int pos) { String tmp = sequence.hashCode() + " " + index + " " + pos; @@ -598,16 +618,25 @@ public class SeqPanel extends JPanel implements MouseListener, if (lastMessage == null || !lastMessage.equals(tmp)) { // System.err.println("mouseOver Sequence: "+tmp); - ssm.mouseOverSequence(sequence, index, pos); + ssm.mouseOverSequence(sequence, index, pos, av); } lastMessage = tmp; } + @Override public void highlightSequence(SearchResults results) { + if (av.followHighlight) + { + if (ap.scrollToPosition(results, false)) + { + seqCanvas.revalidate(); + } + } seqCanvas.highlightSearchResults(results); } + @Override public void updateColours(SequenceI seq, int index) { System.out.println("update the seqPanel colours"); @@ -616,10 +645,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseMoved(MouseEvent evt) { if (editingSeqs) @@ -650,7 +680,7 @@ public class SeqPanel extends JPanel implements MouseListener, tooltipText.setLength(6); // Cuts the buffer back to - SequenceGroup[] groups = av.alignment.findAllGroups(sequence); + SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence); if (groups != null) { for (int g = 0; g < groups.length; g++) @@ -679,42 +709,116 @@ public class SeqPanel extends JPanel implements MouseListener, // use aa to see if the mouse pointer is on a if (av.showSequenceFeatures) { - SequenceFeature[] features = findFeaturesAtRes(sequence - .getDatasetSequence(), sequence.findPosition(res)); + int rpos; + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), + rpos = sequence.findPosition(res)); + appendFeatures(tooltipText, linkImageURL.toString(), rpos, features, + this.ap.seqPanel.seqCanvas.fr.minmax); + } + if (tooltipText.length() == 6) // + { + setToolTipText(null); + lastTooltip = null; + } + else + { + tooltipText.append(""); + if (lastTooltip == null + || !lastTooltip.equals(tooltipText.toString())) + { + setToolTipText(tooltipText.toString()); + lastTooltip = tooltipText.toString(); + } + + } + + } + + private Point lastp = null; + + /* + * (non-Javadoc) + * + * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent) + */ + public Point getToolTipLocation(MouseEvent event) + { + int x = event.getX(), w = getWidth(); + int wdth = (w - x < 200) ? -(w / 2) : 5; // switch sides when tooltip is too + // close to edge + Point p = lastp; + if (!event.isShiftDown() || p == null) + { + p = (tooltipText != null && tooltipText.length() > 6) ? new Point( + event.getX() + wdth, event.getY() - 20) : null; + } + /* + * TODO: try to modify position region is not obcured by tooltip + */ + return lastp = p; + } + + /** + * appends the features at rpos to the given stringbuffer ready for display in + * a tooltip + * + * @param tooltipText2 + * @param linkImageURL + * @param rpos + * @param features + * TODO refactor to Jalview 'utilities' somehow. + */ + public void appendFeatures(StringBuffer tooltipText2, + String linkImageURL, int rpos, SequenceFeature[] features) + { + appendFeatures(tooltipText2, linkImageURL, rpos, features, null); + } - if (features != null) + public void appendFeatures(StringBuffer tooltipText2, String string, + int rpos, SequenceFeature[] features, Hashtable minmax) + { + String tmpString; + if (features != null) + { + for (int i = 0; i < features.length; i++) { - for (int i = 0; i < features.length; i++) + if (features[i].getType().equals("disulfide bond")) { - if (features[i].getType().equals("disulfide bond")) + if (features[i].getBegin() == rpos + || features[i].getEnd() == rpos) { - if (features[i].getBegin() == sequence.findPosition(res) - || features[i].getEnd() == sequence.findPosition(res)) + if (tooltipText2.length() > 6) { - if (tooltipText.length() > 6) - { - tooltipText.append("
"); - } - tooltipText.append("disulfide bond " + features[i].getBegin() - + ":" + features[i].getEnd()); - if (features[i].links != null) - { - tooltipText.append(" "); - } + tooltipText2.append("
"); + } + tooltipText2.append("disulfide bond " + features[i].getBegin() + + ":" + features[i].getEnd()); + if (features[i].links != null) + { + tooltipText2.append(" "); } } - else + } + else + { + if (tooltipText2.length() > 6) { - if (tooltipText.length() > 6) + tooltipText2.append("
"); + } + // TODO: remove this hack to display link only features + boolean linkOnly = features[i].getValue("linkonly") != null; + if (!linkOnly) + { + tooltipText2.append(features[i].getType() + " "); + if (rpos != 0) { - tooltipText.append("
"); + // we are marking a positional feature + tooltipText2.append(features[i].begin); } - - tooltipText.append(features[i].getType() + " " - + features[i].begin); if (features[i].begin != features[i].end) { - tooltipText.append(" " + features[i].end); + tooltipText2.append(" " + features[i].end); } if (features[i].getDescription() != null @@ -722,17 +826,20 @@ public class SeqPanel extends JPanel implements MouseListener, .getType())) { tmpString = features[i].getDescription(); - int startTag = tmpString.toUpperCase().indexOf(""); + String tmp2up=tmpString.toUpperCase(); + int startTag = tmp2up.indexOf(""); if (startTag > -1) { tmpString = tmpString.substring(startTag + 6); + tmp2up = tmp2up.substring(startTag+6); } - int endTag = tmpString.toUpperCase().indexOf(""); + int endTag = tmp2up.indexOf(""); if (endTag > -1) { tmpString = tmpString.substring(0, endTag); + tmp2up = tmp2up.substring(0, endTag); } - endTag = tmpString.toUpperCase().indexOf(""); + endTag = tmp2up.indexOf(""); if (endTag > -1) { tmpString = tmpString.substring(0, endTag); @@ -740,7 +847,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (startTag > -1) { - tooltipText.append("; " + tmpString); + tooltipText2.append("; " + tmpString); } else { @@ -752,63 +859,57 @@ public class SeqPanel extends JPanel implements MouseListener, tmpString = tmpString.replaceAll("<", "<"); tmpString = tmpString.replaceAll(">", ">"); - tooltipText.append("; "); - tooltipText.append(tmpString); + tooltipText2.append("; "); + tooltipText2.append(tmpString); } else { - tooltipText.append("; " + tmpString); + tooltipText2.append("; " + tmpString); } } } + // check score should be shown + if (features[i].getScore() != Float.NaN) + { + float[][] rng = (minmax == null) ? null : ((float[][]) minmax + .get(features[i].getType())); + if (rng != null && rng[0] != null && rng[0][0] != rng[0][1]) + { + tooltipText2.append(" Score=" + features[i].getScore()); + } + } if (features[i].getValue("status") != null) { String status = features[i].getValue("status").toString(); if (status.length() > 0) { - tooltipText.append("; (" + features[i].getValue("status") + tooltipText2.append("; (" + features[i].getValue("status") + ")"); } } - - if (features[i].links != null) - { - tooltipText.append(" "); - } - } + if (features[i].links != null) + { + tooltipText2.append(" "); + } + } } } - - if (tooltipText.length() == 6) // - { - setToolTipText(null); - } - else - { - tooltipText.append(""); - if (lastTooltip == null - || !lastTooltip.equals(tooltipText.toString())) - setToolTipText(tooltipText.toString()); - - lastTooltip = tooltipText.toString(); - } - } String lastTooltip; /** * Set status message in alignment panel - * + * * @param sequence - * aligned sequence object + * aligned sequence object * @param res - * alignment column + * alignment column * @param seq - * index of sequence in alignment + * index of sequence in alignment * @return position of res in sequence */ int setStatusMessage(SequenceI sequence, int res, int seq) @@ -818,7 +919,7 @@ public class SeqPanel extends JPanel implements MouseListener, + sequence.getName()); Object obj = null; - if (av.alignment.isNucleotide()) + if (av.getAlignment().isNucleotide()) { obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) + ""); @@ -850,10 +951,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent evt) { if (mouseWheelPressed) @@ -862,8 +964,7 @@ public class SeqPanel extends JPanel implements MouseListener, // Which is bigger, left-right or up-down? if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt - .getX() - - lastMousePress.getX())) + .getX() - lastMousePress.getX())) { int fontSize = av.font.getSize(); @@ -881,9 +982,7 @@ public class SeqPanel extends JPanel implements MouseListener, fontSize = 1; } - av - .setFont(new Font(av.font.getName(), av.font.getStyle(), - fontSize)); + av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize)); av.charWidth = oldWidth; ap.fontChanged(); } @@ -930,11 +1029,11 @@ public class SeqPanel extends JPanel implements MouseListener, if ((res < av.getAlignment().getWidth()) && (res < lastres)) { // dragLeft, delete gap - editSequence(false, res); + editSequence(false, false,res); } else { - editSequence(true, res); + editSequence(true, false,res); } mouseDragging = true; @@ -944,22 +1043,22 @@ public class SeqPanel extends JPanel implements MouseListener, } } - synchronized void editSequence(boolean insertGap, int startres) + //TODO: Make it more clever than many booleans + synchronized void editSequence(boolean insertGap, boolean editSeq, int startres) { int fixedLeft = -1; int fixedRight = -1; boolean fixedColumns = false; SequenceGroup sg = av.getSelectionGroup(); - SequenceI seq = av.alignment.getSequenceAt(startseq); + SequenceI seq = av.getAlignment().getSequenceAt(startseq); // No group, but the sequence may represent a group - if (!groupEditing && av.hasHiddenRows) + if (!groupEditing && av.hasHiddenRows()) { - if (av.hiddenRepSequences != null - && av.hiddenRepSequences.containsKey(seq)) + if (av.isHiddenRepSequence(seq)) { - sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + sg = av.getRepresentedSequences(seq); groupEditing = true; } } @@ -1001,7 +1100,7 @@ public class SeqPanel extends JPanel implements MouseListener, // Are we editing within a selection group? if (groupEditing - || (sg != null && sg.getSequences(av.hiddenRepSequences) + || (sg != null && sg.getSequences(av.getHiddenRepSequences()) .contains(seq))) { fixedColumns = true; @@ -1010,13 +1109,12 @@ public class SeqPanel extends JPanel implements MouseListener, // but the sequence represents a group if (sg == null) { - if (av.hiddenRepSequences == null - || !av.hiddenRepSequences.containsKey(seq)) + if (!av.isHiddenRepSequence(seq)) { endEditing(); return; } - sg = (SequenceGroup) av.hiddenRepSequences.get(seq); + sg = av.getRepresentedSequences(seq); } fixedLeft = sg.getStartRes(); @@ -1043,7 +1141,7 @@ public class SeqPanel extends JPanel implements MouseListener, } } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { fixedColumns = true; int y1 = av.getColumnSelection().getHiddenBoundaryLeft(startres); @@ -1073,12 +1171,12 @@ public class SeqPanel extends JPanel implements MouseListener, if (groupEditing) { - Vector vseqs = sg.getSequences(av.hiddenRepSequences); + List vseqs = sg.getSequences(av.getHiddenRepSequences()); int g, groupSize = vseqs.size(); SequenceI[] groupSeqs = new SequenceI[groupSize]; for (g = 0; g < groupSeqs.length; g++) { - groupSeqs[g] = (SequenceI) vseqs.elementAt(g); + groupSeqs[g] = vseqs.get(g); } // drag to right @@ -1087,9 +1185,9 @@ public class SeqPanel extends JPanel implements MouseListener, // 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.getEndRes() == av.getAlignment().getWidth() - 1) { - sg.setEndRes(av.alignment.getWidth() + startres - lastres); + sg.setEndRes(av.getAlignment().getWidth() + startres - lastres); fixedRight = sg.getEndRes(); } @@ -1121,19 +1219,19 @@ public class SeqPanel extends JPanel implements MouseListener, if (!blank) { - if (sg.getSize() == av.alignment.getHeight()) + if (sg.getSize() == av.getAlignment().getHeight()) { - if ((av.hasHiddenColumns && startres < av.getColumnSelection() + if ((av.hasHiddenColumns() && startres < av.getColumnSelection() .getHiddenBoundaryRight(startres))) { endEditing(); return; } - int alWidth = av.alignment.getWidth(); - if (av.hasHiddenRows) + int alWidth = av.getAlignment().getWidth(); + if (av.hasHiddenRows()) { - int hwidth = av.alignment.getHiddenSequences().getWidth(); + int hwidth = av.getAlignment().getHiddenSequences().getWidth(); if (hwidth > alWidth) { alWidth = hwidth; @@ -1190,7 +1288,7 @@ public class SeqPanel extends JPanel implements MouseListener, else { editCommand.appendEdit(EditCommand.INSERT_GAP, groupSeqs, - startres, startres - lastres, av.alignment, true); + startres, startres - lastres, av.getAlignment(), true); } } else @@ -1206,7 +1304,7 @@ public class SeqPanel extends JPanel implements MouseListener, else { editCommand.appendEdit(EditCommand.DELETE_GAP, groupSeqs, - startres, lastres - startres, av.alignment, true); + startres, lastres - startres, av.getAlignment(), true); } } @@ -1228,11 +1326,12 @@ public class SeqPanel extends JPanel implements MouseListener, else { editCommand.appendEdit(EditCommand.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres, av.alignment, true); - } + { seq }, lastres, startres - lastres, av.getAlignment(), true); + } } else { + if(!editSeq){ // dragging to the left if (fixedColumns && fixedRight != -1) { @@ -1263,9 +1362,24 @@ public class SeqPanel extends JPanel implements MouseListener, if (max > 0) { editCommand.appendEdit(EditCommand.DELETE_GAP, new SequenceI[] - { seq }, startres, max, av.alignment, true); + { seq }, startres, max, av.getAlignment(), true); } } + }else{//insertGap==false AND editSeq==TRUE; + if (fixedColumns && fixedRight != -1) + { + for (int j = lastres; j < startres; j++) + { + insertChar(j, new SequenceI[] + { seq }, fixedRight); + } + } + else + { + editCommand.appendEdit(EditCommand.INSERT_NUC, new SequenceI[] + { seq }, lastres, startres - lastres, av.getAlignment(), true); + } + } } } @@ -1299,9 +1413,9 @@ public class SeqPanel extends JPanel implements MouseListener, } editCommand.appendEdit(EditCommand.DELETE_GAP, seq, blankColumn, 1, - av.alignment, true); + av.getAlignment(), true); - editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.alignment, + editCommand.appendEdit(EditCommand.INSERT_GAP, seq, j, 1, av.getAlignment(), true); } @@ -1309,19 +1423,20 @@ public class SeqPanel extends JPanel implements MouseListener, void deleteChar(int j, SequenceI[] seq, int fixedColumn) { - editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.alignment, + editCommand.appendEdit(EditCommand.DELETE_GAP, seq, j, 1, av.getAlignment(), true); editCommand.appendEdit(EditCommand.INSERT_GAP, seq, fixedColumn, 1, - av.alignment, true); + av.getAlignment(), true); } /** * DOCUMENT ME! - * + * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent e) { if (oldSeq < 0) @@ -1338,10 +1453,11 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -1355,26 +1471,29 @@ public class SeqPanel extends JPanel implements MouseListener, } } + @Override public void mouseClicked(MouseEvent evt) { - SequenceI sequence = av.alignment.getSequenceAt(findSeq(evt)); + SequenceGroup sg = null; + SequenceI sequence = av.getAlignment().getSequenceAt(findSeq(evt)); if (evt.getClickCount() > 1) { - if (av.getSelectionGroup().getSize() == 1 - && av.getSelectionGroup().getEndRes() - - av.getSelectionGroup().getStartRes() < 2) + sg = av.getSelectionGroup(); + if (sg != null && sg.getSize() == 1 + && sg.getEndRes() - sg.getStartRes() < 2) { av.setSelectionGroup(null); } - SequenceFeature[] features = findFeaturesAtRes(sequence - .getDatasetSequence(), sequence.findPosition(findRes(evt))); + SequenceFeature[] features = findFeaturesAtRes( + sequence.getDatasetSequence(), + sequence.findPosition(findRes(evt))); if (features != null && features.length > 0) { SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features[0].getBegin(), features[0] - .getEnd()); + highlight.addResult(sequence, features[0].getBegin(), + features[0].getEnd()); seqCanvas.highlightSearchResults(highlight); } if (features != null && features.length > 0) @@ -1387,6 +1506,7 @@ public class SeqPanel extends JPanel implements MouseListener, } } + @Override public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); @@ -1398,13 +1518,14 @@ public class SeqPanel extends JPanel implements MouseListener, { ap.scrollUp(true); } + // TODO Update tooltip for new position. } /** * DOCUMENT ME! - * + * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void doMousePressedDefineMode(MouseEvent evt) { @@ -1414,7 +1535,7 @@ public class SeqPanel extends JPanel implements MouseListener, startWrapBlock = wrappedBlock; - if (av.wrapAlignment && seq > av.alignment.getHeight()) + if (av.wrapAlignment && seq > av.getAlignment().getHeight()) { JOptionPane.showInternalMessageDialog(Desktop.desktop, "Cannot edit annotations in wrapped view.", @@ -1427,7 +1548,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); if ((sequence == null) || (res > sequence.getLength())) { @@ -1438,7 +1559,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup == null) { - stretchGroup = av.alignment.findGroup(sequence); + stretchGroup = av.getAlignment().findGroup(sequence); if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) && (res < stretchGroup.getEndRes())) @@ -1456,7 +1577,7 @@ public class SeqPanel extends JPanel implements MouseListener, { stretchGroup = null; - SequenceGroup[] allGroups = av.alignment.findAllGroups(sequence); + SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); if (allGroups != null) { @@ -1477,8 +1598,8 @@ public class SeqPanel extends JPanel implements MouseListener, if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - SequenceFeature[] allFeatures = findFeaturesAtRes(sequence - .getDatasetSequence(), sequence.findPosition(res)); + SequenceFeature[] allFeatures = findFeaturesAtRes( + sequence.getDatasetSequence(), sequence.findPosition(res)); Vector links = new Vector(); for (int i = 0; i < allFeatures.length; i++) { @@ -1514,6 +1635,7 @@ public class SeqPanel extends JPanel implements MouseListener, sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); + stretchGroup = sg; if (av.getConservationSelected()) @@ -1546,9 +1668,9 @@ public class SeqPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void doMouseReleasedDefineMode(MouseEvent evt) { @@ -1557,48 +1679,41 @@ public class SeqPanel extends JPanel implements MouseListener, return; } + stretchGroup.recalcConservation(); // always do this - annotation has own + // state if (stretchGroup.cs != null) { if (stretchGroup.cs instanceof ClustalxColourScheme) { - ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup - .getSequences(av.hiddenRepSequences), stretchGroup - .getWidth()); - } - - if (stretchGroup.cs instanceof Blosum62ColourScheme - || stretchGroup.cs instanceof PIDColourScheme - || stretchGroup.cs.conservationApplied() - || stretchGroup.cs.getThreshold() > 0) - { - stretchGroup.recalcConservation(); + ((ClustalxColourScheme) stretchGroup.cs).alignmentChanged( + stretchGroup,av.getHiddenRepSequences()); } if (stretchGroup.cs.conservationApplied()) { - SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup - .getName()); + SliderPanel.setConservationSlider(ap, stretchGroup.cs, + stretchGroup.getName()); } else { - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup - .getName()); + SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, + stretchGroup.getName()); } - PaintRefresher.Refresh(this, av.getSequenceSetId()); - ap.paintAlignment(true); } + PaintRefresher.Refresh(this, av.getSequenceSetId()); + ap.paintAlignment(true); changeEndRes = false; changeStartRes = false; stretchGroup = null; - + av.sendSelection(); } /** * DOCUMENT ME! - * + * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void doMouseDraggedDefineMode(MouseEvent evt) { @@ -1615,9 +1730,9 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - if (res >= av.alignment.getWidth()) + if (res >= av.getAlignment().getWidth()) { - res = av.alignment.getWidth() - 1; + res = av.getAlignment().getWidth() - 1; } if (stretchGroup.getEndRes() == res) @@ -1662,7 +1777,7 @@ public class SeqPanel extends JPanel implements MouseListener, dragDirection = -1; } - while ((y != oldSeq) && (oldSeq > -1) && (y < av.alignment.getHeight())) + while ((y != oldSeq) && (oldSeq > -1) && (y < av.getAlignment().getHeight())) { // This routine ensures we don't skip any sequences, as the // selection is quite slow. @@ -1753,6 +1868,7 @@ public class SeqPanel extends JPanel implements MouseListener, running = false; } + @Override public void run() { running = true; @@ -1767,7 +1883,7 @@ public class SeqPanel extends JPanel implements MouseListener, } if (mouseDragging && (evt.getY() >= getHeight()) - && (av.alignment.getHeight() > av.getEndSeq())) + && (av.getAlignment().getHeight() > av.getEndSeq())) { running = ap.scrollUp(false); } @@ -1791,4 +1907,100 @@ public class SeqPanel extends JPanel implements MouseListener, } } } + + /** + * modify current selection according to a received message. + */ + @Override + public void selection(SequenceGroup seqsel, ColumnSelection colsel, + SelectionSource source) + { + // TODO: fix this hack - source of messages is align viewport, but SeqPanel + // handles selection messages... + // TODO: extend config options to allow user to control if selections may be + // shared between viewports. + if (av == source + || !av.followSelection + || (av.isSelectionGroupChanged(false) || av.isColSelChanged(false)) + || (source instanceof AlignViewport && ((AlignViewport) source) + .getSequenceSetId().equals(av.getSequenceSetId()))) + { + return; + } + // do we want to thread this ? (contention with seqsel and colsel locks, I + // suspect) + // rules are: colsel is copied if there is a real intersection between + // sequence selection + boolean repaint = false, copycolsel = true; + // if (!av.isSelectionGroupChanged(false)) + { + SequenceGroup sgroup = null; + if (seqsel != null && seqsel.getSize()>0) + { + if (av.getAlignment() == null) + { + jalview.bin.Cache.log.warn("alignviewport av SeqSetId=" + + av.getSequenceSetId() + " ViewId=" + av.getViewId() + + " 's alignment is NULL! returning immediatly."); + return; + } + sgroup = seqsel.intersect(av.getAlignment(), + (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); + if ((sgroup == null || sgroup.getSize() == 0) + || (colsel == null || colsel.size() == 0)) + { + // don't copy columns if the region didn't intersect. + copycolsel = false; + } + } + if (sgroup != null && sgroup.getSize() > 0) + { + av.setSelectionGroup(sgroup); + } + else + { + av.setSelectionGroup(null); + } + av.isSelectionGroupChanged(true); + repaint = true; + } + if (copycolsel) + { + // the current selection is unset or from a previous message + // so import the new colsel. + if (colsel == null || colsel.size() == 0) + { + if (av.getColumnSelection() != null) + { + av.getColumnSelection().clear(); + repaint=true; + } + } + else + { + // TODO: shift colSel according to the intersecting sequences + if (av.getColumnSelection() == null) + { + av.setColumnSelection(new ColumnSelection(colsel)); + } + else + { + av.getColumnSelection().setElementsFrom(colsel); + } + } + av.isColSelChanged(true); + repaint = true; + } + if (copycolsel && av.hasHiddenColumns() + && (av.getColumnSelection() == null || av.getColumnSelection().getHiddenColumns() == null)) + { + System.err.println("Bad things"); + } + if (repaint) + { + // probably finessing with multiple redraws here + PaintRefresher.Refresh(this, av.getSequenceSetId()); + // ap.paintAlignment(false); + } + } }