/* * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) * Copyright (C) $$Year-Rel$$ The Jalview Authors * * 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 . * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; import jalview.analysis.AlignmentUtils; import jalview.bin.JalviewLite; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.util.MessageManager; import jalview.util.ParseHtmlBodyAndLinks; import awt2swing.Checkbox; import awt2swing.CheckboxMenuItem; import java.awt.Color; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.FontMetrics; import awt2swing.Frame; import java.awt.Graphics; import java.awt.Image; import awt2swing.MenuItem; import awt2swing.Panel; import awt2swing.PopupMenu; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.InputEvent; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.util.Arrays; import java.util.Collections; import java.util.Vector; public class AnnotationLabels extends Panel implements ActionListener, MouseListener, MouseMotionListener { Image image; boolean active = false; AlignmentPanel ap; AlignViewport av; boolean resizing = false; int oldY, mouseX; static String ADDNEW = "Add New Row"; static String EDITNAME = "Edit Label/Description"; static String HIDE = "Hide This Row"; static String SHOWALL = "Show All Hidden Rows"; static String OUTPUT_TEXT = "Show Values In Textbox"; static String COPYCONS_SEQ = "Copy Consensus Sequence"; int scrollOffset = 0; int selectedRow = -1; Tooltip tooltip; private boolean hasHiddenRows; public AnnotationLabels(AlignmentPanel ap) { this.ap = ap; this.av = ap.av; setLayout(null); /** * this retrieves the adjustable height glyph from resources. we don't use * it at the moment. java.net.URL url = * getClass().getResource("/images/idwidth.gif"); Image temp = null; * * if (url != null) { temp = * java.awt.Toolkit.getDefaultToolkit().createImage(url); } * * try { MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0); * mt.waitForID(0); } catch (Exception ex) { } * * BufferedImage bi = new BufferedImage(temp.getHeight(this), * temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g = * (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90)); * g.drawImage(temp, 0, -bi.getWidth(this), this); image = (Image) bi; */ addMouseListener(this); addMouseMotionListener(this); } public AnnotationLabels(AlignViewport av) { this.av = av; } public void setScrollOffset(int y, boolean repaint) { scrollOffset = y; if (repaint) { repaint(); } } /** * * @param y * @return -2 if no rows are visible at all, -1 if no visible rows were * selected */ int getSelectedRow(int y) { int row = -2; AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); if (aa == null) { return row; } int height = 0; for (int i = 0; i < aa.length; i++) { row = -1; if (!aa[i].visible) { continue; } height += aa[i].height; if (y < height) { row = i; break; } } return row; } public void actionPerformed(ActionEvent evt) { AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (evt.getActionCommand().equals(ADDNEW)) { AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null, new Annotation[ap.av.getAlignment().getWidth()]); if (!editLabelDescription(newAnnotation)) { return; } ap.av.getAlignment().addAnnotation(newAnnotation); ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); } else if (evt.getActionCommand().equals(EDITNAME)) { editLabelDescription(aa[selectedRow]); } else if (evt.getActionCommand().equals(HIDE)) { aa[selectedRow].visible = false; } else if (evt.getActionCommand().equals(SHOWALL)) { for (int i = 0; i < aa.length; i++) { aa[i].visible = (aa[i].annotations == null) ? false : true; } } else if (evt.getActionCommand().equals(OUTPUT_TEXT)) { CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame); Frame frame = new Frame(); frame.add(cap); JalviewLite.addFrame(frame, ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500, 100); cap.setText(aa[selectedRow].toString()); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { SequenceI cons = av.getConsensusSeq(); if (cons != null) { copy_annotseqtoclipboard(cons); } } refresh(); } /** * Adjust size and repaint */ protected void refresh() { ap.annotationPanel.adjustPanelHeight(); setSize(getSize().width, ap.annotationPanel.getSize().height); ap.validate(); ap.paintAlignment(true); } boolean editLabelDescription(AlignmentAnnotation annotation) { Checkbox padGaps = new Checkbox("Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"", annotation.padGaps); EditNameDialog dialog = new EditNameDialog(annotation.label, annotation.description, " Annotation Label", "Annotation Description", ap.alignFrame, "Edit Annotation Name / Description", 500, 180, false); Panel empty = new Panel(new FlowLayout()); empty.add(padGaps); dialog.add(empty); dialog.pack(); dialog.setVisible(true); if (dialog.accept) { annotation.label = dialog.getName(); annotation.description = dialog.getDescription(); annotation.setPadGaps(padGaps.getState(), av.getGapCharacter()); repaint(); return true; } else { return false; } } boolean resizePanel = false; public void mouseMoved(MouseEvent evt) { resizePanel = evt.getY() < 10 && evt.getX() < 14; int row = getSelectedRow(evt.getY() + scrollOffset); if (row > -1) { ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks( av.getAlignment().getAlignmentAnnotation()[row] .getDescription(true), true, "\n"); if (tooltip == null) { tooltip = new Tooltip(phb.getNonHtmlContent(), this); } else { tooltip.setTip(phb.getNonHtmlContent()); } } else if (tooltip != null) { tooltip.setTip(""); } } /** * curent drag position */ MouseEvent dragEvent = null; /** * flag to indicate drag events should be ignored */ private boolean dragCancelled = false; /** * clear any drag events in progress */ public void cancelDrag() { dragEvent = null; dragCancelled = true; } public void mouseDragged(MouseEvent evt) { if (dragCancelled) { return; } ; dragEvent = evt; if (resizePanel) { Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder .getSize(), f = ap.seqPanelHolder.getSize(); int dif = evt.getY() - oldY; dif /= ap.av.getCharHeight(); dif *= ap.av.getCharHeight(); if ((d.height - dif) > 20 && (f.height + dif) > 20) { ap.annotationPanel.setSize(d.width, d.height - dif); setSize(new Dimension(e.width, d.height - dif)); ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width, d.height - dif)); ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height - dif)); ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0, av.calcPanelHeight()); f.height += dif; ap.seqPanelHolder.setPreferredSize(f); ap.setScrollValues(av.getStartRes(), av.getStartSeq()); ap.validate(); // ap.paintAlignment(true); ap.addNotify(); } } else { int diff; if ((diff = 6 - evt.getY()) > 0) { // nudge scroll up ap.apvscroll.setValue(ap.apvscroll.getValue() - diff); ap.adjustmentValueChanged(null); } else if ((0 < (diff = 6 - ap.annotationSpaceFillerHolder.getSize().height + evt.getY()))) { // nudge scroll down ap.apvscroll.setValue(ap.apvscroll.getValue() + diff); ap.adjustmentValueChanged(null); } repaint(); } } public void mouseClicked(MouseEvent evt) { } public void mouseReleased(MouseEvent evt) { if (!resizePanel && !dragCancelled) { int start = selectedRow; int end = getSelectedRow(evt.getY() + scrollOffset); if (start > -1 && start != end) { // Swap these annotations AlignmentAnnotation startAA = ap.av.getAlignment() .getAlignmentAnnotation()[start]; if (end == -1) { end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; } AlignmentAnnotation endAA = ap.av.getAlignment() .getAlignmentAnnotation()[end]; ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; } } resizePanel = false; dragEvent = null; dragCancelled = false; repaint(); ap.annotationPanel.repaint(); } public void mouseEntered(MouseEvent evt) { if (evt.getY() < 10 && evt.getX() < 14) { resizePanel = true; repaint(); } } public void mouseExited(MouseEvent evt) { dragCancelled = false; if (dragEvent == null) { resizePanel = false; } else { if (!resizePanel) { dragEvent = null; } } repaint(); } public void mousePressed(MouseEvent evt) { oldY = evt.getY(); if (resizePanel) { return; } dragCancelled = false; // todo: move below to mouseClicked ? selectedRow = getSelectedRow(evt.getY() + scrollOffset); AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); // DETECT RIGHT MOUSE BUTTON IN AWT if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { PopupMenu popup = new PopupMenu( MessageManager.getString("label.annotations")); MenuItem item = new MenuItem(ADDNEW); item.addActionListener(this); popup.add(item); if (selectedRow < 0) { // this never happens at moment: - see comment on JAL-563 if (hasHiddenRows) { item = new MenuItem(SHOWALL); item.addActionListener(this); popup.add(item); } this.add(popup); popup.show(this, evt.getX(), evt.getY()); return; } // add the rest if there are actually rows to show item = new MenuItem(EDITNAME); item.addActionListener(this); popup.add(item); item = new MenuItem(HIDE); item.addActionListener(this); popup.add(item); /* * Hide all