X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=aa047d1911a4454b2829fd75d5ad53efbe71c37d;hb=fbfbbe26bee37143d5279fe4d254a5a89c96b021;hp=5242752426129593c03835deffa090cbba865c25;hpb=0eca27bca577e774acd5aefb165e7c6396a1995e;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java index 5242752..aa047d1 100755 --- a/src/jalview/appletgui/AnnotationPanel.java +++ b/src/jalview/appletgui/AnnotationPanel.java @@ -1,1088 +1,791 @@ -/* - * 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 - */ - -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) - { - if (System.getProperty("os.name").startsWith("Mac")) - { - MAC = true; - } - - 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); - - 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 += GRAPH_HEIGHT; - } - - 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[] 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.length() > 0)) - { - int charOffset = (av.charWidth - - fm.charWidth(row.annotations[column]. - displayCharacter.charAt( - 0))) / 2; - 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; - } - - // 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 (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); - - if (sRes == 0) - { - sRes++; - x += av.charWidth; - } - - 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 || aa.annotations[column - 1] == null) - { - x++; - continue; - } - - g.setColor(aa.annotations[column].colour); - 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; - } - - 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) - { - 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++) - { - 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; - } - } -} +/* + * 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.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; + + AlignmentPanel ap; + + int activeRow = -1; + + final String HELIX = "Helix"; + + final String SHEET = "Sheet"; + + /** + * For RNA secondary structure "stems" aka helices + */ + final String STEM = "RNA Helix"; + + final String LABEL = "Label"; + + final String REMOVE = "Remove Annotation"; + + final String COLOUR = "Colour"; + + final Color HELIX_COLOUR = Color.red.darker(); + + final Color SHEET_COLOUR = Color.green.darker().darker(); + + Image image; + + Graphics gg; + + FontMetrics fm; + + int imgWidth = 0; + + 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; + + public final AnnotationRenderer renderer; + + public AnnotationPanel(AlignmentPanel ap) + { + new jalview.util.Platform(); + // MAC = Platform.isAMac(); + this.ap = ap; + av = ap.av; + setLayout(null); + 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) + { + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void actionPerformed(ActionEvent evt) + { + 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]; + System.arraycopy(anot, 0, temp, 0, anot.length); + anot = temp; + aa[activeRow].annotations = anot; + } + + String label = ""; + 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 index : av.getColumnSelection().getSelected()) + { + if (av.getAlignment().getHiddenColumns().isVisible(index)) + { + anot[index] = 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 index : av.getColumnSelection().getSelected()) + { + // TODO: JAL-2001 - provide a fast method to list visible selected + // columns + if (!av.getAlignment().getHiddenColumns().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 index : av.getColumnSelection().getSelected()) + { + if (!av.getAlignment().getHiddenColumns().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"; + } + + // 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; + } + + label = enterLabel(symbol, "Enter Label"); + + if (label == null) + { + return; + } + + if ((label.length() > 0) && !aa[activeRow].hasText) + { + aa[activeRow].hasText = true; + if (evt.getActionCommand().equals(STEM)) + { + aa[activeRow].showAllColLabels = true; + } + } + + for (int index : av.getColumnSelection().getSelected()) + { + if (!av.getAlignment().getHiddenColumns().isVisible(index)) + { + continue; + } + + if (anot[index] == null) + { + anot[index] = new Annotation(label, "", type, 0); + } + + 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(); + + 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; + } + } + + @Override + public void mousePressed(MouseEvent evt) + { + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); + if (aa == null) + { + return; + } + + int height = -scrollOffset; + 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; + } + else if (aa[i].graph != AlignmentAnnotation.NO_GRAPH) + { + // Stretch Graph + graphStretch = i; + graphStretchY = evt.getY(); + } + + break; + } + } + + if ((evt.getModifiersEx() + & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK + && activeRow != -1) + { + if (av.getColumnSelection() == null + || av.getColumnSelection().isEmpty()) + { + return; + } + + 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); + 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; + } + + 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) + { + 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.getAlignment().getAlignmentAnnotation(); + if (aa == null) + { + return; + } + + int row = -1; + int height = -scrollOffset; + for (int i = 0; i < aa.length; i++) + { + + if (aa[i].visible) + { + height += aa[i].height; + } + + if (evt.getY() < height) + { + row = i; + break; + } + } + + int column = evt.getX() / av.getCharWidth() + + av.getRanges().getStartRes(); + + if (av.hasHiddenColumns()) + { + column = av.getAlignment().getHiddenColumns() + .visibleToAbsoluteColumn(column); + } + + if (row > -1 && column < aa[row].annotations.length + && aa[row].annotations[column] != 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(" ").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); + } + + public int adjustPanelHeight() + { + return adjustPanelHeight(true); + } + + public int adjustPanelHeight(boolean repaint) + { + int height = av.calcPanelHeight(); + this.setSize(new Dimension(getSize().width, height)); + if (repaint) + { + 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.getAlignment().getAlignmentAnnotation(); + if (aa == null) + { + return; + } + + for (int j = 0; j < aa.length; j++) + { + if (aa[j].editable) + { + activeRow = j; + break; + } + } + } + } + + @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) + { + 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(); + 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.getRanges().getStartRes(), + av.getRanges().getEndRes() + 1); + + g.drawImage(image, 0, 0, this); + } + + public void fastPaint(int horizontal) + { + 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.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.getCharWidth(); + 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) + { + Font ofont = av.getFont(); + g.setFont(ofont); + + g.setColor(Color.white); + g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), + getSize().height); + + if (fm == null) + { + fm = g.getFontMetrics(); + } + + 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(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); + } + + int scrollOffset = 0; + + public void setScrollOffset(int value, boolean repaint) + { + scrollOffset = value; + if (repaint) + { + repaint(); + } + } + + @Override + public FontMetrics getFontMetrics() + { + return fm; + } + + @Override + public Image getFadedImage() + { + return image; + } + + @Override + public int getFadedImageWidth() + { + 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; + } + } + + @Override + public void propertyChange(PropertyChangeEvent evt) + { + // 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)) + { + fastPaint((int) evt.getNewValue() - (int) evt.getOldValue()); + } + else if (evt.getPropertyName().equals(ViewportRanges.STARTRESANDSEQ)) + { + fastPaint(((int[]) evt.getNewValue())[0] + - ((int[]) evt.getOldValue())[0]); + } + else if (evt.getPropertyName().equals(ViewportRanges.MOVE_VIEWPORT)) + { + repaint(); + } + } +}