X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=aa047d1911a4454b2829fd75d5ad53efbe71c37d;hb=fbfbbe26bee37143d5279fe4d254a5a89c96b021;hp=aef651161be4e7bf7f6670b520e872735f94e6b4;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index aef6511..aa047d1 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -1,32 +1,59 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; - -public class AnnotationPanel extends Panel implements AdjustmentListener, - ActionListener, MouseListener, MouseMotionListener +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.SequenceI; +import jalview.renderer.AnnotationRenderer; +import jalview.renderer.AwtRenderPanelI; +import jalview.schemes.ResidueProperties; +import jalview.util.Comparison; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; + +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Image; +import java.awt.MenuItem; +import java.awt.Panel; +import java.awt.PopupMenu; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.event.InputEvent; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.beans.PropertyChangeEvent; + +public class AnnotationPanel extends Panel + implements AwtRenderPanelI, AdjustmentListener, ActionListener, + MouseListener, MouseMotionListener, ViewportListenerI { AlignViewport av; @@ -34,21 +61,24 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, int activeRow = -1; - Vector activeRes; + final String HELIX = "Helix"; - static String HELIX = "Helix"; + final String SHEET = "Sheet"; - static String SHEET = "Sheet"; + /** + * For RNA secondary structure "stems" aka helices + */ + final String STEM = "RNA Helix"; - static String LABEL = "Label"; + final String LABEL = "Label"; - static String REMOVE = "Remove Annotation"; + final String REMOVE = "Remove Annotation"; - static String COLOUR = "Colour"; + final String COLOUR = "Colour"; - static Color HELIX_COLOUR = Color.red.darker(); + final Color HELIX_COLOUR = Color.red.darker(); - static Color SHEET_COLOUR = Color.green.darker().darker(); + final Color SHEET_COLOUR = Color.green.darker().darker(); Image image; @@ -60,64 +90,92 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, boolean fastPaint = false; + // Used For mouse Dragging and resizing graphs + int graphStretch = -1; + + int graphStretchY = -1; + + boolean mouseDragging = false; + public static int GRAPH_HEIGHT = 40; - boolean MAC = false; + // boolean MAC = false; + + public final AnnotationRenderer renderer; public AnnotationPanel(AlignmentPanel ap) { - MAC = new jalview.util.Platform().isAMac(); + new jalview.util.Platform(); + // MAC = Platform.isAMac(); this.ap = ap; av = ap.av; setLayout(null); - adjustPanelHeight(); + int height = adjustPanelHeight(); + ap.apvscroll.setValues(0, getSize().height, 0, height); addMouseMotionListener(this); addMouseListener(this); // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this ); + renderer = new AnnotationRenderer(); + + av.getRanges().addPropertyChangeListener(this); } public AnnotationPanel(AlignViewport av) { this.av = av; + renderer = new AnnotationRenderer(); + } + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { - ap.alabels.setScrollOffset(-evt.getValue()); } /** * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void actionPerformed(ActionEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); + if (aa == null) + { + return; + } Annotation[] anot = aa[activeRow].annotations; if (anot.length < av.getColumnSelection().getMax()) { - Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2]; + Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + + 2]; System.arraycopy(anot, 0, temp, 0, anot.length); anot = temp; aa[activeRow].annotations = anot; } String label = ""; - if (av.colSel != null && av.colSel.size() > 0 - && anot[av.colSel.getMin()] != null) + if (av.getColumnSelection() != null + && !av.getColumnSelection().isEmpty() + && anot[av.getColumnSelection().getMin()] != null) + { label = anot[av.getColumnSelection().getMin()].displayCharacter; + } if (evt.getActionCommand().equals(REMOVE)) { - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - anot[av.getColumnSelection().columnAt(i)] = null; + if (av.getAlignment().getHiddenColumns().isVisible(index)) + { + anot[index] = null; + } } } else if (evt.getActionCommand().equals(LABEL)) @@ -134,12 +192,14 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, aa[activeRow].hasText = true; } - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - - if (!av.colSel.isVisible(index)) + // TODO: JAL-2001 - provide a fast method to list visible selected + // columns + if (!av.getAlignment().getHiddenColumns().isVisible(index)) + { continue; + } if (anot[index] == null) { @@ -156,12 +216,12 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, Color col = udc.getColor(); - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - - if (!av.colSel.isVisible(index)) + if (!av.getAlignment().getHiddenColumns().isVisible(index)) + { continue; + } if (anot[index] == null) { @@ -187,6 +247,14 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, symbol = "\u03B2"; } + // Added by LML to color stems + else if (evt.getActionCommand().equals(STEM)) + { + type = 'S'; + int column = av.getColumnSelection().getSelectedRanges().get(0)[0]; + symbol = aa[activeRow].getDefaultRnaHelixSymbol(column); + } + if (!aa[activeRow].hasIcons) { aa[activeRow].hasIcons = true; @@ -202,25 +270,33 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, 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++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - - if (!av.colSel.isVisible(index)) + if (!av.getAlignment().getHiddenColumns().isVisible(index)) + { continue; + } if (anot[index] == null) { anot[index] = new Annotation(label, "", type, 0); } - anot[index].secondaryStructure = type; + anot[index].secondaryStructure = type != 'S' ? type + : label.length() == 0 ? ' ' : label.charAt(0); anot[index].displayCharacter = label; } } + av.getAlignment().validateAnnotation(aa[activeRow]); + + ap.alignmentChanged(); adjustPanelHeight(); repaint(); @@ -233,20 +309,25 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, ap.alignFrame, "Enter Label", 400, 200, true); if (dialog.accept) + { return dialog.getName(); + } else + { return null; + } } + @Override public void mousePressed(MouseEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { return; } - int height = 0; + int height = -scrollOffset; activeRow = -1; for (int i = 0; i < aa.length; i++) @@ -262,26 +343,46 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, { activeRow = i; } + else if (aa[i].graph != AlignmentAnnotation.NO_GRAPH) + { + // Stretch Graph + graphStretch = i; + graphStretchY = evt.getY(); + } break; } } - if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK + if ((evt.getModifiersEx() + & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK && activeRow != -1) { - if (av.getColumnSelection() == null) + if (av.getColumnSelection() == null + || av.getColumnSelection().isEmpty()) { 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; + + if (av.getAlignment().isNucleotide()) + { + 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); @@ -297,38 +398,67 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, return; } - if (aa == null) - { - return; - } - ap.scalePanel.mousePressed(evt); } + @Override public void mouseReleased(MouseEvent evt) { + graphStretch = -1; + graphStretchY = -1; + mouseDragging = false; + if (needValidating) + { + ap.validate(); + needValidating = false; + } ap.scalePanel.mouseReleased(evt); } + @Override public void mouseClicked(MouseEvent evt) { } + boolean needValidating = false; + + @Override public void mouseDragged(MouseEvent evt) { - ap.scalePanel.mouseDragged(evt); + if (graphStretch > -1) + { + av.getAlignment() + .getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY + - evt.getY(); + if (av.getAlignment() + .getAlignmentAnnotation()[graphStretch].graphHeight < 0) + { + av.getAlignment() + .getAlignmentAnnotation()[graphStretch].graphHeight = 0; + } + graphStretchY = evt.getY(); + av.calcPanelHeight(); + needValidating = true; + // TODO: only update overview visible geometry + ap.paintAlignment(true, false); + } + else + { + ap.scalePanel.mouseDragged(evt); + } } + @Override public void mouseMoved(MouseEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { return; } int row = -1; - int height = 0; + int height = -scrollOffset; for (int i = 0; i < aa.length; i++) { @@ -344,30 +474,81 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, } } - int res = evt.getX() / av.getCharWidth() + av.getStartRes(); + int column = evt.getX() / av.getCharWidth() + + av.getRanges().getStartRes(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { - res = av.getColumnSelection().adjustForHiddenColumns(res); + column = av.getAlignment().getHiddenColumns() + .visibleToAbsoluteColumn(column); } - if (row > -1 && res < aa[row].annotations.length - && aa[row].annotations[res] != null) + if (row > -1 && column < aa[row].annotations.length + && aa[row].annotations[column] != null) { - StringBuffer text = new StringBuffer("Sequence position " + (res + 1)); - if (aa[row].annotations[res].description != null) + StringBuilder text = new StringBuilder(); + text.append(MessageManager.getString("label.column")).append(" ") + .append(column + 1); + String description = aa[row].annotations[column].description; + if (description != null && description.length() > 0) { - text.append(" " + aa[row].annotations[res].description); + text.append(" ").append(description); } + + /* + * if the annotation is sequence-specific, show the sequence number + * in the alignment, and (if not a gap) the residue and position + */ + SequenceI seqref = aa[row].sequenceRef; + if (seqref != null) + { + int seqIndex = av.getAlignment().findIndex(seqref); + if (seqIndex != -1) + { + text.append(", ") + .append(MessageManager.getString("label.sequence")) + .append(" ").append(seqIndex + 1); + char residue = seqref.getCharAt(column); + if (!Comparison.isGap(residue)) + { + text.append(" "); + String name; + if (av.getAlignment().isNucleotide()) + { + name = ResidueProperties.nucleotideName + .get(String.valueOf(residue)); + text.append(" Nucleotide: ") + .append(name != null ? name : residue); + } + else + { + name = 'X' == residue ? "X" + : ('*' == residue ? "STOP" + : ResidueProperties.aa2Triplet + .get(String.valueOf(residue))); + text.append(" Residue: ") + .append(name != null ? name : residue); + } + int residuePos = seqref.findPosition(column); + text.append(" (").append(residuePos).append(")"); + // int residuePos = seqref.findPosition(column); + // text.append(residue).append(" (") + // .append(residuePos).append(")"); + } + } + } + ap.alignFrame.statusBar.setText(text.toString()); } } + @Override public void mouseEntered(MouseEvent evt) { ap.scalePanel.mouseEntered(evt); } + @Override public void mouseExited(MouseEvent evt) { ap.scalePanel.mouseExited(evt); @@ -375,62 +556,32 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, public int adjustPanelHeight() { - // 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; - } + return adjustPanelHeight(true); + } - height += aa[i].height; - } - } - else + public int adjustPanelHeight(boolean repaint) + { + int height = av.calcPanelHeight(); + this.setSize(new Dimension(getSize().width, height)); + if (repaint) { - height = 20; + repaint(); } - - this.setSize(getSize().width, height); - - repaint(); - return height; - } + /** + * calculate the height for visible annotation, revalidating bounds where + * necessary ABSTRACT GUI METHOD + * + * @return total height of annotation + */ + public void addEditableColumn(int i) { if (activeRow == -1) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { return; @@ -445,31 +596,28 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, } } } - - if (activeRes == null) - { - activeRes = new Vector(); - activeRes.addElement(String.valueOf(i)); - return; - } - - activeRes.addElement(String.valueOf(i)); } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { - - imgWidth = getSize().width; + Dimension d = getSize(); + imgWidth = d.width; // (av.endRes - av.startRes + 1) * av.charWidth; - - if (image == null || imgWidth != image.getWidth(this)) + if (imgWidth < 1 || d.height < 1) { - image = createImage(imgWidth, ap.annotationPanel.getSize().height); + return; + } + if (image == null || imgWidth != image.getWidth(this) + || d.height != image.getHeight(this)) + { + image = createImage(imgWidth, d.height); gg = image.getGraphics(); gg.setFont(av.getFont()); fm = gg.getFontMetrics(); @@ -485,27 +633,30 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, gg.setColor(Color.white); gg.fillRect(0, 0, getSize().width, getSize().height); - drawComponent(gg, av.startRes, av.endRes + 1); + drawComponent(gg, av.getRanges().getStartRes(), + av.getRanges().getEndRes() + 1); g.drawImage(image, 0, 0, this); } public void fastPaint(int horizontal) { - if (horizontal == 0 || av.alignment.getAlignmentAnnotation() == null - || av.alignment.getAlignmentAnnotation().length < 1) + if (horizontal == 0 || gg == null + || av.getAlignment().getAlignmentAnnotation() == null + || av.getAlignment().getAlignmentAnnotation().length < 1) { repaint(); return; } - gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal - * av.charWidth, 0); - int sr = av.startRes, er = av.endRes + 1, transX = 0; + gg.copyArea(0, 0, imgWidth, getSize().height, + -horizontal * av.getCharWidth(), 0); + int sr = av.getRanges().getStartRes(), + er = av.getRanges().getEndRes() + 1, transX = 0; if (horizontal > 0) // scrollbar pulled right, image to the left { - transX = (er - sr - horizontal) * av.charWidth; + transX = (er - sr - horizontal) * av.getCharWidth(); sr = er - horizontal; } else if (horizontal < 0) @@ -527,580 +678,114 @@ public class AnnotationPanel extends Panel implements AdjustmentListener, * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param startRes - * DOCUMENT ME! + * DOCUMENT ME! * @param endRes - * DOCUMENT ME! + * DOCUMENT ME! */ public void drawComponent(Graphics g, int startRes, int endRes) { - g.setFont(av.getFont()); + Font ofont = av.getFont(); + g.setFont(ofont); g.setColor(Color.white); - g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height); + g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), + getSize().height); if (fm == null) { 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; } + g.translate(0, -scrollOffset); + renderer.drawComponent(this, av, g, activeRow, startRes, endRes); + g.translate(0, +scrollOffset); + } - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - - int x = 0; - int y = 0; - int column = 0; - char lastSS; - int lastSSX; - int iconOffset = av.charHeight / 2; - boolean validRes = false; - boolean validEnd = false; - boolean[] graphGroupDrawn = new boolean[aa.length]; + int scrollOffset = 0; - // \u03B2 \u03B1 - for (int i = 0; i < aa.length; i++) + public void setScrollOffset(int value, boolean repaint) + { + scrollOffset = value; + if (repaint) { - AlignmentAnnotation row = aa[i]; - - if (!row.visible) - { - continue; - } - - lastSS = ' '; - lastSSX = 0; - - if (row.graph > 0) - { - if (row.graphGroup > -1 && graphGroupDrawn[row.graphGroup]) - { - continue; - } - - // this is so that we draw the characters below the graph - y += row.height; - - if (row.hasText) - { - y -= av.charHeight; - } - } - - if (row.hasText) - { - iconOffset = av.charHeight / 2; - } - else - { - iconOffset = 0; - } - - x = 0; - while (x < endRes - startRes) - { - if (av.hasHiddenColumns) - { - column = av.getColumnSelection().adjustForHiddenColumns( - startRes + x); - if (column > row.annotations.length - 1) - { - break; - } - } - else - { - column = startRes + x; - } - - if ((row.annotations.length <= column) - || (row.annotations[column] == null)) - { - validRes = false; - } - else - { - validRes = true; - } - - if (activeRow == i) - { - g.setColor(Color.red); - - if (av.getColumnSelection() != null) - { - for (int n = 0; n < av.getColumnSelection().size(); n++) - { - int v = av.getColumnSelection().columnAt(n); - - if (v == column) - { - g - .fillRect(x * av.charWidth, y, av.charWidth, - av.charHeight); - } - } - } - } - - if (av.validCharWidth - && validRes - && (row.annotations[column].displayCharacter != null && row.annotations[column].displayCharacter - .length() > 0)) - { - int charOffset = (av.getCentreColumnLabels()) ? ((av.charWidth - fm - .charsWidth(row.annotations[column].displayCharacter - .toCharArray(), 0, - row.annotations[column].displayCharacter.length())) / 2) - : (av.charWidth - fm - .charWidth(row.annotations[column].displayCharacter - .charAt(0))) / 2; - - if (row.annotations[column].colour == null) - g.setColor(Color.black); - else - g.setColor(row.annotations[column].colour); - - if (column == 0 || row.graph > 0) - { - g.drawString(row.annotations[column].displayCharacter, - (x * av.charWidth) + charOffset, y + iconOffset + 3); - } - else if (row.annotations[column - 1] == null - || (!row.annotations[column].displayCharacter - .equals(row.annotations[column - 1].displayCharacter) || (row.annotations[column].displayCharacter - .length() < 2 && row.annotations[column].secondaryStructure == ' '))) - { - g.drawString(row.annotations[column].displayCharacter, - (x * av.charWidth) + charOffset, y + iconOffset + 3); - } - } - - if (row.hasIcons) - { - if (!validRes - || (row.annotations[column].secondaryStructure != lastSS)) - { - switch (lastSS) - { - case 'H': - g.setColor(HELIX_COLOUR); - if (MAC) - { - // Off by 1 offset when drawing rects and ovals - // to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, - (x * av.charWidth) - lastSSX, 7, 8, 8); - break; - } - - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - - if (sCol == 0 - || row.annotations[sCol - 1] == null - || row.annotations[sCol - 1].secondaryStructure != 'H') - { - g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90, - 180); - x1 += av.charWidth / 2; - } - - if (row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'H') - { - g.fillArc((x * av.charWidth) - av.charWidth, y + 4 - + iconOffset, av.charWidth, 8, 270, 180); - x2 -= av.charWidth / 2; - } - - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); - break; - - case 'E': - g.setColor(SHEET_COLOUR); - g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - - lastSSX - 4, 7); - g.fillPolygon(new int[] - { (x * av.charWidth) - 4, (x * av.charWidth) - 4, - (x * av.charWidth) }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, - 3); - - break; - - default: - g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); - - break; - } - - if (validRes) - { - lastSS = row.annotations[column].secondaryStructure; - } - else - { - lastSS = ' '; - } - - lastSSX = (x * av.charWidth); - } - } - - column++; - x++; - } - - if (column >= row.annotations.length) - { - column = row.annotations.length - 1; - validEnd = false; - } - else - { - validEnd = true; - } - - // x ++; - - if (row.hasIcons) - { - switch (lastSS) - { - case 'H': - g.setColor(HELIX_COLOUR); - if (MAC) - { - // Off by 1 offset when drawing rects and ovals - // to offscreen image on the MAC - g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - - lastSSX, 7, 8, 8); - break; - } - - int sCol = (lastSSX / av.charWidth) + startRes; - int x1 = lastSSX; - int x2 = (x * av.charWidth); - - if (sCol == 0 || row.annotations[sCol - 1] == null - || row.annotations[sCol - 1].secondaryStructure != 'H') - { - g - .fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, - 90, 180); - x1 += av.charWidth / 2; - } - - if (row.annotations[column] == null - || row.annotations[column].secondaryStructure != 'H') - { - g.fillArc((x * av.charWidth) - av.charWidth, - y + 4 + iconOffset, av.charWidth, 8, 270, 180); - x2 -= av.charWidth / 2; - } - - g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8); - - break; - - case 'E': - g.setColor(SHEET_COLOUR); - - if (!validEnd || row.annotations[endRes] == null - || row.annotations[endRes].secondaryStructure != 'E') - { - g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth) - - lastSSX - 4, 7); - g.fillPolygon(new int[] - { (x * av.charWidth) - 4, (x * av.charWidth) - 4, - (x * av.charWidth) }, new int[] - { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3); - } - else - { - g.fillRect(lastSSX, y + 4 + iconOffset, x * av.charWidth - - lastSSX, 7); - } - break; - - default: - g.setColor(Color.gray); - if (!av.wrapAlignment || endRes == av.endRes) - { - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); - } - - break; - } - } - - if (row.graph > 0) - { - if (row.graph == AlignmentAnnotation.LINE_GRAPH) - { - if (row.graphGroup > -1 && !graphGroupDrawn[row.graphGroup]) - { - float groupmax = -999999, groupmin = 9999999; - for (int gg = 0; gg < aa.length; gg++) - { - if (aa[gg].graphGroup != row.graphGroup) - { - continue; - } - - if (aa[gg] != row) - { - aa[gg].visible = false; - } - - if (aa[gg].graphMax > groupmax) - { - groupmax = aa[gg].graphMax; - } - if (aa[gg].graphMin < groupmin) - { - groupmin = aa[gg].graphMin; - } - } - - for (int gg = 0; gg < aa.length; gg++) - { - if (aa[gg].graphGroup == row.graphGroup) - { - drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin, - groupmax, row.graphHeight); - } - } - - graphGroupDrawn[row.graphGroup] = true; - } - else - { - drawLineGraph(g, row, startRes, endRes, y, row.graphMin, - row.graphMax, row.graphHeight); - } - } - else if (row.graph == AlignmentAnnotation.BAR_GRAPH) - { - drawBarGraph(g, row, startRes, endRes, row.graphMin, - row.graphMax, y); - } - } - - if (row.graph > 0 && row.hasText) - { - y += av.charHeight; - } - - if (row.graph == 0) - { - y += aa[i].height; - } + repaint(); } } - public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, - int eRes, int y, float min, float max, int graphHeight) + @Override + public FontMetrics getFontMetrics() { - if (sRes > aa.annotations.length) - { - return; - } - - int x = 0; - - // Adjustment for fastpaint to left - if (eRes < av.endRes) - { - eRes++; - } - - eRes = Math.min(eRes, aa.annotations.length); - - int y1 = y, y2 = y; - float range = max - min; - - // //Draw origin - if (min < 0) - { - y2 = y - (int) ((0 - min / range) * graphHeight); - } + return fm; + } - g.setColor(Color.gray); - g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2); + @Override + public Image getFadedImage() + { + return image; + } - eRes = Math.min(eRes, aa.annotations.length); + @Override + public int getFadedImageWidth() + { + return imgWidth; + } - int column; - int aaMax = aa.annotations.length - 1; + private int[] bounds = new int[2]; - while (x < eRes - sRes) + @Override + public int[] getVisibleVRange() + { + if (ap != null && ap.alabels != null) { - column = sRes + x; - if (av.hasHiddenColumns) - { - column = av.getColumnSelection().adjustForHiddenColumns(column); - } - - if (column > aaMax) - { - break; - } - - if (aa.annotations[column] == null) // || coaa.annotations[column - 1] == - // null) - { - x++; - continue; - } - - if (aa.annotations[column].colour == null) - g.setColor(Color.black); - else - g.setColor(aa.annotations[column].colour); - if (column == 0 || aa.annotations[column - 1] == null) - { - y1 = y - - (int) (((aa.annotations[column].value - min) / range) * graphHeight); - } - else - { - y1 = y - - (int) (((aa.annotations[column - 1].value - min) / range) * graphHeight); - } - y2 = y - - (int) (((aa.annotations[column].value - min) / range) * graphHeight); - - g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth - + av.charWidth / 2, y2); - x++; + int sOffset = -ap.alabels.scrollOffset; + int visHeight = sOffset + ap.annotationPanelHolder.getHeight(); + bounds[0] = sOffset; + bounds[1] = visHeight; + return bounds; } - - if (aa.threshold != null) + else { - g.setColor(aa.threshold.colour); - - y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight); - g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); + return null; } } - public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, - int eRes, float min, float max, int y) + @Override + public void propertyChange(PropertyChangeEvent evt) { - if (sRes > aa.annotations.length) - { - return; - } - - eRes = Math.min(eRes, aa.annotations.length); - - int x = 0, y1 = y, y2 = y; - - float range = max - min; - - if (min < 0) - { - y2 = y - (int) ((0 - min / (range)) * aa.graphHeight); - } - - g.setColor(Color.gray); - - g.drawLine(x, y2, (eRes - sRes) * av.charWidth, y2); - - int column; - int aaMax = aa.annotations.length - 1; - - while (x < eRes - sRes) + // Respond to viewport range changes (e.g. alignment panel was scrolled) + // Both scrolling and resizing change viewport ranges: scrolling changes + // both start and end points, but resize only changes end values. + // Here we only want to fastpaint on a scroll, with resize using a normal + // paint, so scroll events are identified as changes to the horizontal or + // vertical start value. + if (evt.getPropertyName().equals(ViewportRanges.STARTRES)) { - column = sRes + x; - if (av.hasHiddenColumns) - { - column = av.getColumnSelection().adjustForHiddenColumns(column); - } - - if (column > aaMax) - { - break; - } - - if (aa.annotations[column] == null) - { - x++; - continue; - } - - if (aa.annotations[column].colour == null) - g.setColor(Color.black); - else - g.setColor(aa.annotations[column].colour); - - y1 = y - - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight); - - if (y1 - y2 > 0) - { - g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2); - } - else - { - g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1); - } - - x++; - + fastPaint((int) evt.getNewValue() - (int) evt.getOldValue()); } - if (aa.threshold != null) + else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)) { - g.setColor(aa.threshold.colour); - y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight); - g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); + fastPaint(((int[]) evt.getNewValue())[0] + - ((int[]) evt.getOldValue())[0]); } - } - - // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, - int y, int sRes, int eRes) - { - eRes = Math.min(eRes, aa.annotations.length); - g.setColor(Color.white); - g.fillRect(0, 0, width, y); - g.setColor(new Color(0, 0, 180)); - - int x = 0, height; - - for (int j = sRes; j < eRes; j++) + else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT)) { - if (aa.annotations[j].colour == null) - g.setColor(Color.black); - else - g.setColor(aa.annotations[j].colour); - - height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT); - if (height > y) - { - height = y; - } - g.fillRect(x, y - height, av.charWidth, height); - x += av.charWidth; + repaint(); } } }