X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=a343bcfcf1f4e814e3c34d116a9f83d6c36ee048;hb=7335eb77076ba83a2faebeaf45f0aa03407fdcd1;hp=f068a3cc35405cd9af13cf73ac7910a6536e0d5a;hpb=4e6c8d302a9df7012789e755e23d7a9b3f5d35bf;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index f068a3c..a343bcf 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -1,19 +1,20 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 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; @@ -21,17 +22,15 @@ import java.util.*; import java.awt.*; import java.awt.event.*; -import java.awt.font.LineMetrics; -import java.awt.geom.AffineTransform; -import jalview.analysis.AAFrequency; import jalview.datamodel.*; import jalview.renderer.AnnotationRenderer; import jalview.renderer.AwtRenderPanelI; -import jalview.schemes.ColourSchemeI; +import jalview.util.MessageManager; -public class AnnotationPanel extends Panel implements AwtRenderPanelI, AdjustmentListener, - ActionListener, MouseListener, MouseMotionListener +public class AnnotationPanel extends Panel implements AwtRenderPanelI, + AdjustmentListener, ActionListener, MouseListener, + MouseMotionListener { AlignViewport av; @@ -41,19 +40,24 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen Vector activeRes; - static String HELIX = "Helix"; + final String HELIX = "Helix"; - static String SHEET = "Sheet"; + final String SHEET = "Sheet"; - static String LABEL = "Label"; + /** + * For RNA secondary structure "stems" aka helices + */ + final String STEM = "RNA Helix"; - static String REMOVE = "Remove Annotation"; + final String LABEL = "Label"; - static String COLOUR = "Colour"; + final String REMOVE = "Remove Annotation"; - static Color HELIX_COLOUR = Color.red.darker(); + final String COLOUR = "Colour"; - static Color SHEET_COLOUR = Color.green.darker().darker(); + final Color HELIX_COLOUR = Color.red.darker(); + + final Color SHEET_COLOUR = Color.green.darker().darker(); Image image; @@ -101,6 +105,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen renderer = new AnnotationRenderer(); } + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { } @@ -111,9 +116,10 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen * @param evt * DOCUMENT ME! */ + @Override public void actionPerformed(ActionEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { return; @@ -129,8 +135,9 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen } String label = ""; - if (av.colSel != null && av.colSel.size() > 0 - && anot[av.colSel.getMin()] != null) + if (av.getColumnSelection() != null + && av.getColumnSelection().size() > 0 + && anot[av.getColumnSelection().getMin()] != null) label = anot[av.getColumnSelection().getMin()].displayCharacter; if (evt.getActionCommand().equals(REMOVE)) @@ -158,7 +165,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen { int index = av.getColumnSelection().columnAt(i); - if (!av.colSel.isVisible(index)) + if (!av.getColumnSelection().isVisible(index)) continue; if (anot[index] == null) @@ -180,7 +187,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen { int index = av.getColumnSelection().columnAt(i); - if (!av.colSel.isVisible(index)) + if (!av.getColumnSelection().isVisible(index)) continue; if (anot[index] == null) @@ -207,6 +214,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen symbol = "\u03B2"; } + // Added by LML to color stems + else if (evt.getActionCommand().equals(STEM)) + { + type = 'S'; + symbol = "\u03C3"; + } + if (!aa[activeRow].hasIcons) { aa[activeRow].hasIcons = true; @@ -222,13 +236,17 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen if ((label.length() > 0) && !aa[activeRow].hasText) { aa[activeRow].hasText = true; + if (evt.getActionCommand().equals(STEM)) + { + aa[activeRow].showAllColLabels=true; + } } for (int i = 0; i < av.getColumnSelection().size(); i++) { int index = av.getColumnSelection().columnAt(i); - if (!av.colSel.isVisible(index)) + if (!av.getColumnSelection().isVisible(index)) continue; if (anot[index] == null) @@ -241,6 +259,9 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen } } + av.getAlignment().validateAnnotation(aa[activeRow]); + + ap.alignmentChanged(); adjustPanelHeight(); repaint(); @@ -258,9 +279,10 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen return null; } + @Override public void mousePressed(MouseEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { return; @@ -301,13 +323,26 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen return; } - PopupMenu pop = new PopupMenu("Structure type"); - MenuItem item = new MenuItem(HELIX); - item.addActionListener(this); - pop.add(item); - item = new MenuItem(SHEET); - item.addActionListener(this); - pop.add(item); + PopupMenu pop = new PopupMenu(MessageManager.getString("label.structure_type")); + MenuItem item; + /* + * Just display the needed structure options + */ + if (av.getAlignment().isNucleotide() == true) + { + item = new MenuItem(STEM); + item.addActionListener(this); + pop.add(item); + } + else + { + item = new MenuItem(HELIX); + item.addActionListener(this); + pop.add(item); + item = new MenuItem(SHEET); + item.addActionListener(this); + pop.add(item); + } item = new MenuItem(LABEL); item.addActionListener(this); pop.add(item); @@ -331,6 +366,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen ap.scalePanel.mousePressed(evt); } + @Override public void mouseReleased(MouseEvent evt) { graphStretch = -1; @@ -344,24 +380,26 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen ap.scalePanel.mouseReleased(evt); } + @Override public void mouseClicked(MouseEvent evt) { } boolean needValidating = false; + @Override public void mouseDragged(MouseEvent evt) { if (graphStretch > -1) { - av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY + av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY(); - if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0) + if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0) { - av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0; + av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0; } graphStretchY = evt.getY(); - calcPanelHeight(); + av.calcPanelHeight(); needValidating = true; ap.paintAlignment(true); } @@ -371,9 +409,10 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen } } + @Override public void mouseMoved(MouseEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { return; @@ -398,7 +437,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen int res = evt.getX() / av.getCharWidth() + av.getStartRes(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { res = av.getColumnSelection().adjustForHiddenColumns(res); } @@ -415,11 +454,13 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen } } + @Override public void mouseEntered(MouseEvent evt) { ap.scalePanel.mouseEntered(evt); } + @Override public void mouseExited(MouseEvent evt) { ap.scalePanel.mouseExited(evt); @@ -432,7 +473,7 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen public int adjustPanelHeight(boolean repaint) { - int height = calcPanelHeight(); + int height = av.calcPanelHeight(); this.setSize(new Dimension(getSize().width, height)); if (repaint) { @@ -440,65 +481,19 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen } return height; } + /** - * calculate the height for visible annotation, revalidating bounds where necessary - * ABSTRACT GUI METHOD + * calculate the height for visible annotation, revalidating bounds where + * necessary ABSTRACT GUI METHOD + * * @return total height of annotation */ - public int calcPanelHeight() - { - // setHeight of panels - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int height = 0; - - if (aa != null) - { - for (int i = 0; i < aa.length; i++) - { - if (!aa[i].visible) - { - continue; - } - - aa[i].height = 0; - - if (aa[i].hasText) - { - aa[i].height += av.charHeight; - } - - if (aa[i].hasIcons) - { - aa[i].height += 16; - } - - if (aa[i].graph > 0) - { - aa[i].height += aa[i].graphHeight; - } - - if (aa[i].height == 0) - { - aa[i].height = 20; - } - - height += aa[i].height; - } - } - if (height == 0) - { - height = 20; - } - - return height; - - } public void addEditableColumn(int i) { if (activeRow == -1) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { return; @@ -524,21 +519,24 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen activeRes.addElement(String.valueOf(i)); } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { Dimension d = getSize(); imgWidth = d.width; // (av.endRes - av.startRes + 1) * av.charWidth; - if (imgWidth<1 || d.height<1) + if (imgWidth < 1 || d.height < 1) { return; } - if (image == null || imgWidth != image.getWidth(this) || d.height != image.getHeight(this)) + if (image == null || imgWidth != image.getWidth(this) + || d.height != image.getHeight(this)) { image = createImage(imgWidth, d.height); gg = image.getGraphics(); @@ -563,8 +561,9 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen public void fastPaint(int horizontal) { - if (horizontal == 0 || av.alignment.getAlignmentAnnotation() == null - || av.alignment.getAlignmentAnnotation().length < 1) + if (horizontal == 0 + || av.getAlignment().getAlignmentAnnotation() == null + || av.getAlignment().getAlignmentAnnotation().length < 1) { repaint(); return; @@ -617,15 +616,15 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen fm = g.getFontMetrics(); } - if ((av.alignment.getAlignmentAnnotation() == null) - || (av.alignment.getAlignmentAnnotation().length < 1)) + if ((av.getAlignment().getAlignmentAnnotation() == null) + || (av.getAlignment().getAlignmentAnnotation().length < 1)) { g.setColor(Color.white); g.fillRect(0, 0, getSize().width, getSize().height); g.setColor(Color.black); if (av.validCharWidth) { - g.drawString("Alignment has no annotations", 20, 15); + g.drawString(MessageManager.getString("label.alignment_has_no_annotations"), 20, 15); } return; @@ -634,13 +633,16 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen renderer.drawComponent(this, av, g, activeRow, startRes, endRes); g.translate(0, +scrollOffset); } - + int scrollOffset = 0; - public void setScrollOffset(int value) + public void setScrollOffset(int value, boolean repaint) { scrollOffset = value; - repaint(); + if (repaint) + { + repaint(); + } } @Override @@ -660,4 +662,16 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI, Adjustmen { return imgWidth; } + private int[] bounds = new int[2]; + @Override + public int[] getVisibleVRange() + { + if (ap!=null && ap.alabels!=null) + { + int sOffset=-ap.alabels.scrollOffset; + int visHeight = sOffset+ap.annotationPanelHolder.getHeight(); + bounds[0] = sOffset; bounds[1]=visHeight; + return bounds; + } else return null; + } }