/* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) * Copyright (C) 2008 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 */ 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 { AlignViewport av; AlignmentPanel ap; int activeRow = -1; Vector activeRes; static String HELIX = "Helix"; static String SHEET = "Sheet"; static String LABEL = "Label"; static String REMOVE = "Remove Annotation"; static String COLOUR = "Colour"; static Color HELIX_COLOUR = Color.red.darker(); static Color SHEET_COLOUR = Color.green.darker().darker(); Image image; Graphics gg; FontMetrics fm; int imgWidth = 0; boolean fastPaint = false; public static int GRAPH_HEIGHT = 40; boolean MAC = false; public AnnotationPanel(AlignmentPanel ap) { MAC = new jalview.util.Platform().isAMac(); this.ap = ap; av = ap.av; setLayout(null); adjustPanelHeight(); addMouseMotionListener(this); addMouseListener(this); // ap.annotationScroller.getVAdjustable().addAdjustmentListener( this ); } public AnnotationPanel(AlignViewport av) { this.av = av; } public void adjustmentValueChanged(AdjustmentEvent evt) { ap.alabels.setScrollOffset( -evt.getValue()); } /** * DOCUMENT ME! * * @param evt DOCUMENT ME! */ public void actionPerformed(ActionEvent evt) { AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); Annotation[] anot = aa[activeRow].annotations; if (anot.length < av.getColumnSelection().getMax()) { 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) label = anot[av.getColumnSelection().getMin()].displayCharacter; if (evt.getActionCommand().equals(REMOVE)) { for (int i = 0; i < av.getColumnSelection().size(); i++) { anot[av.getColumnSelection().columnAt(i)] = null; } } else if (evt.getActionCommand().equals(LABEL)) { label = enterLabel(label, "Enter Label"); if (label == null) { return; } if ( (label.length() > 0) && !aa[activeRow].hasText) { aa[activeRow].hasText = true; } for (int i = 0; i < av.getColumnSelection().size(); i++) { int index = av.getColumnSelection().columnAt(i); if(!av.colSel.isVisible(index)) continue; if (anot[index] == null) { anot[index] = new Annotation(label, "", ' ', 0); } anot[index].displayCharacter = label; } } else if (evt.getActionCommand().equals(COLOUR)) { UserDefinedColours udc = new UserDefinedColours( this, Color.black, ap.alignFrame); Color col = udc.getColor(); for (int i = 0; i < av.getColumnSelection().size(); i++) { int index = av.getColumnSelection().columnAt(i); if(!av.colSel.isVisible(index)) continue; if (anot[index] == null) { anot[index] = new Annotation("", "", ' ', 0); } anot[index].colour = col; } } else // HELIX OR SHEET { char type = 0; String symbol = "\u03B1"; if (evt.getActionCommand().equals(HELIX)) { type = 'H'; } else if (evt.getActionCommand().equals(SHEET)) { type = 'E'; symbol = "\u03B2"; } if (!aa[activeRow].hasIcons) { aa[activeRow].hasIcons = true; } label = enterLabel(symbol, "Enter Label"); if (label == null) { return; } if ( (label.length() > 0) && !aa[activeRow].hasText) { aa[activeRow].hasText = true; } for (int i = 0; i < av.getColumnSelection().size(); i++) { int index = av.getColumnSelection().columnAt(i); if(!av.colSel.isVisible(index)) continue; if (anot[index] == null) { anot[index] = new Annotation(label, "", type, 0); } anot[index].secondaryStructure = type; anot[index].displayCharacter = label; } } adjustPanelHeight(); repaint(); return; } String enterLabel(String text, String label) { EditNameDialog dialog = new EditNameDialog(text,null,label,null, ap.alignFrame,"Enter Label", 400,200, true); if(dialog.accept) return dialog.getName(); else return null; } public void mousePressed(MouseEvent evt) { AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); if (aa == null) { return; } int height = 0; activeRow = -1; for (int i = 0; i < aa.length; i++) { if (aa[i].visible) { height += aa[i].height; } if (evt.getY() < height) { if (aa[i].editable) { activeRow = i; } break; } } if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK && activeRow != -1) { if (av.getColumnSelection() == null) { 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); item = new MenuItem(LABEL); item.addActionListener(this); pop.add(item); item = new MenuItem(COLOUR); item.addActionListener(this); pop.add(item); item = new MenuItem(REMOVE); item.addActionListener(this); pop.add(item); ap.alignFrame.add(pop); pop.show(this, evt.getX(), evt.getY()); return; } if (aa == null) { return; } ap.scalePanel.mousePressed(evt); } public void mouseReleased(MouseEvent evt) { ap.scalePanel.mouseReleased(evt); } public void mouseClicked(MouseEvent evt) {} public void mouseDragged(MouseEvent evt) { ap.scalePanel.mouseDragged(evt); } public void mouseMoved(MouseEvent evt) { AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); if (aa == null) { return; } int row = -1; int height = 0; for (int i = 0; i < aa.length; i++) { if (aa[i].visible) { height += aa[i].height; } if (evt.getY() < height) { row = i; break; } } int res = evt.getX() / av.getCharWidth() + av.getStartRes(); if (av.hasHiddenColumns) { res = av.getColumnSelection().adjustForHiddenColumns(res); } if (row > -1 && res < aa[row].annotations.length && aa[row].annotations[res] != null) { StringBuffer text = new StringBuffer("Sequence position " + (res + 1)); if (aa[row].annotations[res].description != null) { text.append(" " + aa[row].annotations[res].description); } ap.alignFrame.statusBar.setText(text.toString()); } } public void mouseEntered(MouseEvent evt) { ap.scalePanel.mouseEntered(evt); } public void mouseExited(MouseEvent evt) { ap.scalePanel.mouseExited(evt); } 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; } height += aa[i].height; } } else { height = 20; } this.setSize(getSize().width, height); repaint(); return height; } public void addEditableColumn(int i) { if (activeRow == -1) { AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); if (aa == null) { return; } for (int j = 0; j < aa.length; j++) { if (aa[j].editable) { activeRow = j; break; } } } if (activeRes == null) { activeRes = new Vector(); activeRes.addElement(String.valueOf(i)); return; } activeRes.addElement(String.valueOf(i)); } public void update(Graphics g) { paint(g); } public void paint(Graphics g) { imgWidth = getSize().width; //(av.endRes - av.startRes + 1) * av.charWidth; if (image == null || imgWidth != image.getWidth(this)) { image = createImage(imgWidth, ap.annotationPanel.getSize().height); gg = image.getGraphics(); gg.setFont(av.getFont()); fm = gg.getFontMetrics(); fastPaint = false; } if (fastPaint) { g.drawImage(image, 0, 0, this); fastPaint = false; return; } gg.setColor(Color.white); gg.fillRect(0, 0, getSize().width, getSize().height); drawComponent(gg, av.startRes, av.endRes + 1); g.drawImage(image, 0, 0, this); } public void fastPaint(int horizontal) { if (horizontal == 0 || av.alignment.getAlignmentAnnotation() == null || av.alignment.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; if (horizontal > 0) // scrollbar pulled right, image to the left { transX = (er - sr - horizontal) * av.charWidth; sr = er - horizontal; } else if (horizontal < 0) { er = sr - horizontal; } gg.translate(transX, 0); drawComponent(gg, sr, er); gg.translate( -transX, 0); fastPaint = true; repaint(); } /** * DOCUMENT ME! * * @param g DOCUMENT ME! * @param startRes DOCUMENT ME! * @param endRes DOCUMENT ME! */ public void drawComponent(Graphics g, int startRes, int endRes) { g.setFont(av.getFont()); g.setColor(Color.white); g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height); if (fm == null) { fm = g.getFontMetrics(); } if ( (av.alignment.getAlignmentAnnotation() == null) || (av.alignment.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); } return; } 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]; //\u03B2 \u03B1 for (int i = 0; i < aa.length; i++) { 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; } } } public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, int y, float min, float max, int graphHeight) { 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); } g.setColor(Color.gray); g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2); eRes = Math.min(eRes, aa.annotations.length); int column; int aaMax = aa.annotations.length - 1; while (x < eRes - sRes) { 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++; } if (aa.threshold != null) { g.setColor(aa.threshold.colour); y2 = (int) (y - ( (aa.threshold.value - min) / range) * graphHeight); g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); } } public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, int eRes, float min, float max, int y) { 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) { 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++; } if (aa.threshold != null) { g.setColor(aa.threshold.colour); y2 = (int) (y - ( (aa.threshold.value - min) / range) * aa.graphHeight); g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); } } // 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++) { 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; } } }