X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=d2832f84f93305d101787cbc5974a6179c36c1fb;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=44a03ecaef810a93012ca9cb9a69d5b560f9924d;hpb=5d01e85b903f9ce67b2b4a32e9e7a02f57d9f2e9;p=jalview.git diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index 44a03ec..d2832f8 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -1,43 +1,49 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 + * 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 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.appletgui; import java.awt.*; import java.awt.event.*; +import java.util.Vector; import jalview.datamodel.*; import jalview.util.UrlLink; -public class IdPanel - extends Panel implements MouseListener, MouseMotionListener +public class IdPanel extends Panel implements MouseListener, + MouseMotionListener { protected IdCanvas idCanvas; + protected AlignViewport av; + protected AlignmentPanel alignPanel; + ScrollThread scrollThread = null; int offy; + int width; + int lastid = -1; + boolean mouseDragging = false; + java.util.Vector links = new java.util.Vector(); public IdPanel(AlignViewport av, AlignmentPanel parent) @@ -51,6 +57,7 @@ public class IdPanel idCanvas.addMouseMotionListener(this); String label, url; + // TODO: add in group link parameter if (av.applet != null) { for (int i = 1; i < 10; i++) @@ -73,33 +80,93 @@ public class IdPanel } Tooltip tooltip; + public void mouseMoved(MouseEvent e) { int seq = alignPanel.seqPanel.findSeq(e); SequenceI sequence = av.getAlignment().getSequenceAt(seq); - if (sequence.getDescription() == null) + // look for non-pos features + StringBuffer tooltiptext = new StringBuffer(); + if (sequence != null) + { + if (sequence.getDescription() != null) + { + tooltiptext.append(sequence.getDescription()); + tooltiptext.append("\n"); + } + + SequenceFeature sf[] = sequence.getSequenceFeatures(); + for (int sl = 0; sf != null && sl < sf.length; sl++) + { + if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) + { + boolean nl = false; + if (sf[sl].getFeatureGroup() != null) + { + tooltiptext.append(sf[sl].getFeatureGroup()); + nl = true; + } + ; + if (sf[sl].getType() != null) + { + tooltiptext.append(" "); + tooltiptext.append(sf[sl].getType()); + nl = true; + } + ; + if (sf[sl].getDescription() != null) + { + tooltiptext.append(" "); + tooltiptext.append(sf[sl].getDescription()); + nl = true; + } + ; + if (sf[sl].getScore() != Float.NaN && sf[sl].getScore() != 0f) + { + tooltiptext.append(" Score = "); + tooltiptext.append(sf[sl].getScore()); + nl = true; + } + ; + if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0) + { + tooltiptext.append(" ("); + tooltiptext.append(sf[sl].getStatus()); + tooltiptext.append(")"); + nl = true; + } + ; + if (nl) + { + tooltiptext.append("\n"); + } + } + } + } + if (tooltiptext.length() == 0) { + // nothing to display - so clear tooltip if one is visible if (tooltip != null) { tooltip.setVisible(false); } tooltip = null; + tooltiptext = null; return; } - if (tooltip == null) { - tooltip = new Tooltip( - sequence.getDisplayId(true) - + "\n" + sequence.getDescription(), idCanvas); + tooltip = new Tooltip(sequence.getDisplayId(true) + "\n" + + tooltiptext.toString(), idCanvas); } else { - tooltip.setTip(sequence.getDisplayId(true) - + "\n" + sequence.getDescription()); + tooltip.setTip(sequence.getDisplayId(true) + "\n" + + tooltiptext.toString()); } + tooltiptext = null; } public void mouseDragged(MouseEvent e) @@ -128,13 +195,18 @@ public class IdPanel return; } - //DEFAULT LINK IS FIRST IN THE LINK LIST + // DEFAULT LINK IS FIRST IN THE LINK LIST int seq = alignPanel.seqPanel.findSeq(e); - String id = av.getAlignment().getSequenceAt(seq).getName(); - + SequenceI sq = av.getAlignment().getSequenceAt(seq); + if (sq==null) + { + return; + } + String id = sq.getName(); + String target = null; String url = null; - int i=0; + int i = 0; while (url == null && i < links.size()) { // DEFAULT LINK IS FIRST IN THE LINK LIST @@ -161,7 +233,7 @@ public class IdPanel } String urls[] = urlLink.makeUrls(id, true); - if (urls == null || urls[0]==null || urls[0].length()<1) + if (urls == null || urls[0] == null || urls[0].length() < 1) { url = null; continue; @@ -173,8 +245,7 @@ public class IdPanel { alignPanel.alignFrame.showURL(url, target); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } @@ -200,8 +271,8 @@ public class IdPanel scrollThread = new ScrollThread(true); } - if (mouseDragging && e.getY() >= getSize().height && - av.alignment.getHeight() > av.getEndSeq()) + if (mouseDragging && e.getY() >= getSize().height + && av.alignment.getHeight() > av.getEndSeq()) { scrollThread = new ScrollThread(false); } @@ -222,19 +293,41 @@ public class IdPanel int seq = alignPanel.seqPanel.findSeq(e); - if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) == - InputEvent.BUTTON3_MASK) + if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { - APopupMenu popup = new APopupMenu(alignPanel, - (Sequence) av.getAlignment(). - getSequenceAt(seq), links); + Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq); + + // build a new links menu based on the current links + any non-positional + // features + Vector nlinks = new Vector(); + for (int l = 0, lSize = links.size(); l < lSize; l++) + { + nlinks.addElement(links.elementAt(l)); + } + SequenceFeature sf[] = sq==null ? null:sq.getSequenceFeatures(); + for (int sl = 0; sf != null && sl < sf.length; sl++) + { + if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0) + { + if (sf[sl].links != null && sf[sl].links.size() > 0) + { + for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++) + { + nlinks.addElement(sf[sl].links.elementAt(l)); + } + } + } + } + + APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks); this.add(popup); popup.show(this, e.getX(), e.getY()); return; } - if ( (av.getSelectionGroup() == null) || - ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null)) + if ((av.getSelectionGroup() == null) + || ((!e.isControlDown() && !e.isShiftDown()) && av + .getSelectionGroup() != null)) { av.setSelectionGroup(new SequenceGroup()); av.getSelectionGroup().setStartRes(0); @@ -277,10 +370,14 @@ public class IdPanel end = tmp; lastid = end; } - + if (av.getSelectionGroup() == null) + { + av.setSelectionGroup(new SequenceGroup()); + } for (int i = start; i <= end; i++) { - av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false); + av.getSelectionGroup().addSequence( + av.getAlignment().getSequenceAt(i), false); } } @@ -299,6 +396,8 @@ public class IdPanel mouseDragging = false; PaintRefresher.Refresh(this, av.getSequenceSetId()); + // always send selection message when mouse is released + av.sendSelection(); } public void highlightSearchResults(java.util.Vector found) @@ -310,7 +409,7 @@ public class IdPanel return; } - int index = av.alignment.findIndex( (SequenceI) found.elementAt(0)); + int index = av.alignment.findIndex((SequenceI) found.elementAt(0)); // do we need to scroll the panel? if (av.getStartSeq() > index || av.getEndSeq() < index) @@ -320,11 +419,12 @@ public class IdPanel } // this class allows scrolling off the bottom of the visible alignment - class ScrollThread - extends Thread + class ScrollThread extends Thread { boolean running = false; + boolean up = true; + public ScrollThread(boolean up) { this.up = up; @@ -370,9 +470,9 @@ public class IdPanel try { Thread.sleep(100); + } catch (Exception ex) + { } - catch (Exception ex) - {} } } }