X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=7a2ecf769c989a0f7f4167efea398fffc39e586b;hb=b9fbdac95abae11673f09be76494032ec0bbca74;hp=1732291321a910a1e2ab4fc70a72cd6359692f0e;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 1732291..7a2ecf7 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,34 +1,36 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * + * 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 + * 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. - * - * 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 + * + * 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.awt.*; import java.awt.event.*; +import java.util.List; import java.util.Vector; import javax.swing.*; import jalview.datamodel.*; +import jalview.io.SequenceAnnotationReport; import jalview.util.UrlLink; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ @@ -51,10 +53,11 @@ public class IdPanel extends JPanel implements MouseListener, int lastid = -1; boolean mouseDragging = false; + private final SequenceAnnotationReport seqAnnotReport; /** * Creates a new IdPanel object. - * + * * @param av * DOCUMENT ME! * @param parent @@ -66,6 +69,7 @@ public class IdPanel extends JPanel implements MouseListener, alignPanel = parent; idCanvas = new IdCanvas(av); linkImageURL = getClass().getResource("/images/link.gif").toString(); + seqAnnotReport = new SequenceAnnotationReport(linkImageURL); setLayout(new BorderLayout()); add(idCanvas, BorderLayout.CENTER); addMouseListener(this); @@ -73,83 +77,36 @@ public class IdPanel extends JPanel implements MouseListener, addMouseWheelListener(this); ToolTipManager.sharedInstance().registerComponent(this); } - /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void mouseMoved(MouseEvent e) { SeqPanel sp = alignPanel.seqPanel; int seq = Math.max(0, sp.findSeq(e)); - String tmp; - if (seq > -1 && seq < av.alignment.getHeight()) + if (seq > -1 && seq < av.getAlignment().getHeight()) { - SequenceI sequence = av.alignment.getSequenceAt(seq); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); StringBuffer tip = new StringBuffer(); - tip.append(""); - - int maxWidth = 0; - if (sequence.getDescription() != null) - { - tmp = sequence.getDescription(); - tip.append("
" + tmp); - maxWidth = Math.max(maxWidth, tmp.length()); - } - - DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef(); - if (av.isShowDbRefs() && dbrefs != null) - { - for (int i = 0; i < dbrefs.length; i++) - { - tip.append("
"); - tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId(); - tip.append(tmp); - maxWidth = Math.max(maxWidth, tmp.length()); - } - } - - // ADD NON POSITIONAL SEQUENCE INFO - SequenceFeature[] features = sequence.getDatasetSequence() - .getSequenceFeatures(); - SequenceFeature[] tfeat = new SequenceFeature[1]; - if (av.isShowNpFeats() && features != null) - { - for (int i = 0; i < features.length; i++) - { - if (features[i].begin == 0 && features[i].end == 0) - { - int sz = -tip.length(); - tfeat[0] = features[i]; - sp.appendFeatures(tip, linkImageURL, 0, tfeat, - sp.seqCanvas.fr.minmax); - sz += tip.length(); - maxWidth = Math.max(maxWidth, sz); - } - } - } - - if (maxWidth > 60) - { - tip.insert(0, "
"); - tip.append("
"); - } - - tip.append(""); - + seqAnnotReport.createSequenceAnnotationReport(tip, sequence, + av.isShowDbRefs(), av.isShowNpFeats(), + sp.seqCanvas.fr.minmax); setToolTipText("" + sequence.getDisplayId(true) + " " - + tip.toString()); + + tip.toString()+""); } } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent e) { mouseDragging = true; @@ -169,25 +126,38 @@ public class IdPanel extends JPanel implements MouseListener, alignPanel.paintAlignment(true); } + @Override public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); if (e.getWheelRotation() > 0) { - alignPanel.scrollUp(false); + if (e.isShiftDown()) + { + alignPanel.scrollRight(true); + + } else { + alignPanel.scrollUp(false); + } } else { - alignPanel.scrollUp(true); + if (e.isShiftDown()) + { + alignPanel.scrollRight(false); + } else { + alignPanel.scrollUp(true); + } } } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void mouseClicked(MouseEvent e) { if (e.getClickCount() < 2) @@ -256,10 +226,11 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent e) { if (scrollThread != null) @@ -270,10 +241,11 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -287,7 +259,7 @@ public class IdPanel extends JPanel implements MouseListener, } if (mouseDragging && (e.getY() >= getHeight()) - && (av.alignment.getHeight() > av.getEndSeq())) + && (av.getAlignment().getHeight() > av.getEndSeq())) { scrollThread = new ScrollThread(false); } @@ -295,10 +267,11 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent e) { if (e.getClickCount() == 2) @@ -342,7 +315,7 @@ public class IdPanel extends JPanel implements MouseListener, { av.setSelectionGroup(new SequenceGroup()); av.getSelectionGroup().setStartRes(0); - av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1); + av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1); } if (e.isShiftDown() && (lastid != -1)) @@ -358,7 +331,7 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param seq * DOCUMENT ME! */ @@ -372,7 +345,7 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param start * DOCUMENT ME! * @param end @@ -403,16 +376,17 @@ public class IdPanel extends JPanel implements MouseListener, for (int i = start; i <= end; i++) { av.getSelectionGroup().addSequence( - av.getAlignment().getSequenceAt(i), true); + av.getAlignment().getSequenceAt(i), i==end); } } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent e) { if (scrollThread != null) @@ -428,20 +402,20 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * - * @param found + * + * @param list * DOCUMENT ME! */ - public void highlightSearchResults(java.util.Vector found) + public void highlightSearchResults(List list) { - idCanvas.setHighlighted(found); + idCanvas.setHighlighted(list); - if (found == null) + if (list == null) { return; } - int index = av.alignment.findIndex((SequenceI) found.get(0)); + int index = av.getAlignment().findIndex(list.get(0)); // do we need to scroll the panel? if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) @@ -468,6 +442,7 @@ public class IdPanel extends JPanel implements MouseListener, running = false; } + @Override public void run() { running = true;