X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=ca5d7f7be2a2ba74bf6cddd90cc029cb0aeb28e9;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=63a57f88a06c29348a93e9991a25454ef4debb60;hpb=18d83f9b01878aec525abf3e4a58da6c0e5e77c2;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java old mode 100755 new mode 100644 index 63a57f8..ca5d7f7 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, 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 file is part of Jalview. * - * 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. + * 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 3 of the License, or (at your option) any later version. * - * 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 + * 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; @@ -22,6 +21,7 @@ import java.util.*; import java.awt.*; import java.awt.event.*; + import javax.swing.*; import jalview.commands.*; @@ -33,10 +33,11 @@ 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!! */ @@ -98,9 +99,9 @@ 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 +123,9 @@ 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); } } @@ -166,6 +168,11 @@ 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(); } @@ -196,8 +203,8 @@ 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.alignment.getHeight() - 1); } else { @@ -455,6 +462,7 @@ public class SeqPanel extends JPanel implements MouseListener, } ap.paintAlignment(false); + av.sendSelection(); } void insertGapAtCursor(boolean group) @@ -520,7 +528,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseReleased(MouseEvent evt) { @@ -540,7 +548,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mousePressed(MouseEvent evt) { @@ -598,13 +606,20 @@ 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; } public void highlightSequence(SearchResults results) { + if (av.followHighlight) + { + if (ap.scrollToPosition(results, false)) + { + seqCanvas.revalidate(); + } + } seqCanvas.highlightSearchResults(results); } @@ -618,7 +633,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseMoved(MouseEvent evt) { @@ -680,35 +695,73 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.showSequenceFeatures) { int rpos; - SequenceFeature[] features = findFeaturesAtRes(sequence - .getDatasetSequence(), rpos = sequence.findPosition(res)); - appendFeatures(tooltipText, linkImageURL.toString(), rpos, features); + 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(); + } - 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 + * 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. + * TODO refactor to Jalview 'utilities' somehow. */ - public static void appendFeatures(StringBuffer tooltipText2, String linkImageURL, - int rpos, SequenceFeature[] features) + public void appendFeatures(StringBuffer tooltipText2, + String linkImageURL, int rpos, SequenceFeature[] features) + { + appendFeatures(tooltipText2, linkImageURL, rpos, features, null); + } + + public void appendFeatures(StringBuffer tooltipText2, String string, + int rpos, SequenceFeature[] features, Hashtable minmax) { String tmpString; if (features != null) @@ -738,73 +791,89 @@ public class SeqPanel extends JPanel implements MouseListener, { tooltipText2.append("
"); } - - tooltipText2.append(features[i].getType() + " "); - if (rpos!=0) - { - // we are marking a positional feature - tooltipText2.append(features[i].begin); - } - if (features[i].begin != features[i].end) + // TODO: remove this hack to display link only features + boolean linkOnly = features[i].getValue("linkonly") != null; + if (!linkOnly) { - tooltipText2.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) + tooltipText2.append(features[i].getType() + " "); + if (rpos != 0) { - tmpString = tmpString.substring(startTag + 6); + // we are marking a positional feature + tooltipText2.append(features[i].begin); } - int endTag = tmpString.toUpperCase().indexOf(""); - if (endTag > -1) + if (features[i].begin != features[i].end) { - tmpString = tmpString.substring(0, endTag); - } - endTag = tmpString.toUpperCase().indexOf(""); - if (endTag > -1) - { - tmpString = tmpString.substring(0, endTag); + tooltipText2.append(" " + features[i].end); } - if (startTag > -1) - { - tooltipText2.append("; " + tmpString); - } - else + if (features[i].getDescription() != null + && !features[i].description.equals(features[i] + .getType())) { - if (tmpString.indexOf("<") > -1 - || tmpString.indexOf(">") > -1) + tmpString = features[i].getDescription(); + String tmp2up=tmpString.toUpperCase(); + int startTag = tmp2up.indexOf(""); + if (startTag > -1) { - // The description does not specify html is to - // be used, so we must remove < > symbols - tmpString = tmpString.replaceAll("<", "<"); - tmpString = tmpString.replaceAll(">", ">"); - - tooltipText2.append("; "); - tooltipText2.append(tmpString); + tmpString = tmpString.substring(startTag + 6); + tmp2up = tmp2up.substring(startTag+6); + } + int endTag = tmp2up.indexOf(""); + if (endTag > -1) + { + tmpString = tmpString.substring(0, endTag); + tmp2up = tmp2up.substring(0, endTag); + } + endTag = tmp2up.indexOf(""); + if (endTag > -1) + { + tmpString = tmpString.substring(0, endTag); + } + if (startTag > -1) + { + tooltipText2.append("; " + tmpString); } else { - tooltipText2.append("; " + tmpString); + 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(">", ">"); + + tooltipText2.append("; "); + tooltipText2.append(tmpString); + + } + else + { + tooltipText2.append("; " + tmpString); + } } } - } - if (features[i].getValue("status") != null) - { - String status = features[i].getValue("status").toString(); - if (status.length() > 0) + // check score should be shown + if (features[i].getScore() != Float.NaN) { - tooltipText2.append("; (" + features[i].getValue("status") - + ")"); + 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) + { + tooltipText2.append("; (" + features[i].getValue("status") + + ")"); + } } } - if (features[i].links != null) { tooltipText2.append(" "); @@ -821,11 +890,11 @@ public class SeqPanel extends JPanel implements MouseListener, * 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) @@ -869,7 +938,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseDragged(MouseEvent evt) { @@ -879,8 +948,7 @@ 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(); @@ -898,9 +966,7 @@ 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(); } @@ -1337,7 +1403,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseEntered(MouseEvent e) { @@ -1357,7 +1423,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void mouseExited(MouseEvent e) { @@ -1374,24 +1440,26 @@ public class SeqPanel extends JPanel implements MouseListener, public void mouseClicked(MouseEvent evt) { + SequenceGroup sg = null; SequenceI sequence = av.alignment.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) @@ -1415,13 +1483,14 @@ 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) { @@ -1494,8 +1563,8 @@ 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++) { @@ -1531,6 +1600,7 @@ public class SeqPanel extends JPanel implements MouseListener, sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); + stretchGroup = sg; if (av.getConservationSelected()) @@ -1565,7 +1635,7 @@ public class SeqPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void doMouseReleasedDefineMode(MouseEvent evt) { @@ -1574,48 +1644,42 @@ 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).resetClustalX( + stretchGroup.getSequences(av.hiddenRepSequences), + stretchGroup.getWidth()); } 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) { @@ -1808,4 +1872,99 @@ public class SeqPanel extends JPanel implements MouseListener, } } } + + /** + * modify current selection according to a received message. + */ + 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.alignment == 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.alignment, + (av.hasHiddenRows) ? av.hiddenRepSequences : 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.colSel != null) + { + av.colSel.clear(); + repaint=true; + } + } + else + { + // TODO: shift colSel according to the intersecting sequences + if (av.colSel == null) + { + av.colSel = new ColumnSelection(colsel); + } + else + { + av.colSel.setElementsFrom(colsel); + } + } + av.isColSelChanged(true); + repaint = true; + } + if (copycolsel && av.hasHiddenColumns + && (av.colSel == null || av.colSel.getHiddenColumns() == null)) + { + System.err.println("Bad things"); + } + if (repaint) + { + // probably finessing with multiple redraws here + PaintRefresher.Refresh(this, av.getSequenceSetId()); + // ap.paintAlignment(false); + } + } }