X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=844c1abfaa242c082fa7ad624df27783e2bd4421;hb=9f08afb8654d8e19fddfd3c6de0e8702804ea97d;hp=50c9fefc37787473c7123850b781bb24478cbeb3;hpb=b14411143cbfb4d311f68b3d3b73a645bf8200e8;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 50c9fef..844c1ab 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 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 @@ -18,744 +18,1246 @@ */ package jalview.gui; -import java.util.*; +import jalview.datamodel.*; import java.awt.*; import java.awt.event.*; import java.awt.image.*; + import javax.swing.*; -import jalview.datamodel.*; -public class AnnotationPanel - extends JPanel implements MouseListener, +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class AnnotationPanel extends JPanel implements MouseListener, MouseMotionListener, ActionListener, AdjustmentListener { - 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(); - - public static int GRAPH_HEIGHT = 40; - AlignViewport av; - AlignmentPanel ap; - int activeRow = -1; - ArrayList activeRes; - BufferedImage image; - Graphics2D gg; - FontMetrics fm; - int imgWidth = 0; - boolean fastPaint = false; - - public AnnotationPanel(AlignmentPanel ap) - { - ToolTipManager.sharedInstance().registerComponent(this); - ToolTipManager.sharedInstance().setInitialDelay(0); - ToolTipManager.sharedInstance().setDismissDelay(10000); - this.ap = ap; - av = ap.av; - this.setLayout(null); - addMouseListener(this); - addMouseMotionListener(this); - ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this); - } - - public void adjustmentValueChanged(AdjustmentEvent evt) - { - ap.alabels.setScrollOffset( -evt.getValue()); - } - - public void adjustPanelHeight() - { - // setHeight of panels - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int height = 0; - - if (aa != null) + final String HELIX = "Helix"; + final String SHEET = "Sheet"; + 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(); + + /** DOCUMENT ME!! */ + AlignViewport av; + AlignmentPanel ap; + int activeRow = -1; + BufferedImage image; + BufferedImage fadedImage; + Graphics2D gg; + FontMetrics fm; + int imgWidth = 0; + boolean fastPaint = false; + + //Used For mouse Dragging and resizing graphs + int graphStretch = -1; + int graphStretchY = -1; + int min; //used by mouseDragged to see if user + int max; //used by mouseDragged to see if user + boolean mouseDragging = false; + + boolean MAC = false; + + /** + * Creates a new AnnotationPanel object. + * + * @param ap DOCUMENT ME! + */ + public AnnotationPanel(AlignmentPanel ap) { - for (int i = 0; i < aa.length; i++) - { - if (!aa[i].visible) - { - continue; - } - aa[i].height = 0; + if(System.getProperty("os.name").startsWith("Mac")) + MAC = true; + + ToolTipManager.sharedInstance().registerComponent(this); + ToolTipManager.sharedInstance().setInitialDelay(0); + ToolTipManager.sharedInstance().setDismissDelay(10000); + this.ap = ap; + av = ap.av; + this.setLayout(null); + addMouseListener(this); + addMouseMotionListener(this); + ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this); + } - if (aa[i].hasText) - { - aa[i].height += av.charHeight; - } + public AnnotationPanel(AlignViewport av) + { + this.av = av; + } - if (aa[i].hasIcons) - { - aa[i].height += 16; - } - if (aa[i].isGraph) + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void adjustmentValueChanged(AdjustmentEvent evt) + { + ap.alabels.setScrollOffset(-evt.getValue()); + } + + /** + * DOCUMENT ME! + */ + public int adjustPanelHeight() + { + // setHeight of panels + image = null; + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + int height = 0; + + if (aa != null) { - aa[i].height += GRAPH_HEIGHT; + 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 (aa[i].height == 0) + else { - aa[i].height = 20; + height = 20; } - height += aa[i].height; - } - } - else - { - height = 20; + this.setPreferredSize(new Dimension(1, height)); + + return height; } - this.setPreferredSize(new Dimension(1, height)); - } - public void addEditableColumn(int i) - { - if (activeRow == -1) + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void actionPerformed(ActionEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + Annotation[] anot = aa[activeRow].annotations; - for (int j = 0; j < aa.length; j++) - { - if (aa[j].editable) + if (evt.getActionCommand().equals(REMOVE)) { - activeRow = j; - - break; + for (int i = 0; i < av.getColumnSelection().size(); i++) + { + anot[av.getColumnSelection().columnAt(i)] = null; + } } - } - } - - if (activeRes == null) - { - activeRes = new ArrayList(); - activeRes.add(String.valueOf(i)); + else if (evt.getActionCommand().equals(LABEL)) + { + String label = JOptionPane.showInputDialog(this, "Enter Label ", + "Enter label", JOptionPane.QUESTION_MESSAGE); - return; - } + if (label == null) + { + return; + } - activeRes.add(String.valueOf(i)); - } + if ((label.length() > 0) && !aa[activeRow].hasText) + { + aa[activeRow].hasText = true; + } - public void actionPerformed(ActionEvent evt) - { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - Annotation[] anot = aa[activeRow].annotations; + for (int i = 0; i < av.getColumnSelection().size(); i++) + { + int index = av.getColumnSelection().columnAt(i); - if (evt.getActionCommand().equals(REMOVE)) - { - for (int i = 0; i < activeRes.size(); i++) - { - anot[Integer.parseInt(activeRes.get(i).toString())] = null; - anot[Integer.parseInt(activeRes.get(i).toString())] = null; - } - } - else if (evt.getActionCommand().equals(LABEL)) - { - String label = JOptionPane.showInputDialog(this, "Enter Label ", - "Enter label", - JOptionPane.QUESTION_MESSAGE); + if (anot[index] == null) + { + anot[index] = new Annotation(label, "", ' ', 0); + } - if (label == null) - { - label = ""; - } + anot[index].displayCharacter = label; + } + } + else if (evt.getActionCommand().equals(COLOUR)) + { + Color col = JColorChooser.showDialog(this, + "Choose foreground colour", Color.black); - 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); - for (int i = 0; i < activeRes.size(); i++) - { - int index = Integer.parseInt(activeRes.get(i).toString()); + if (anot[index] == null) + { + anot[index] = new Annotation("", "", ' ', 0); + } - if (anot[index] == null) - { - anot[index] = new Annotation(label, "", ' ', 0); + anot[index].colour = col; + } } + else // HELIX OR SHEET + { + char type = 0; + String symbol = "\u03B1"; - anot[index].displayCharacter = label; - } - } - else if (evt.getActionCommand().equals(COLOUR)) - { - Color col = JColorChooser.showDialog(this, - "Choose foreground colour", - Color.black); + if (evt.getActionCommand().equals(HELIX)) + { + type = 'H'; + } + else if (evt.getActionCommand().equals(SHEET)) + { + type = 'E'; + symbol = "\u03B2"; + } - for (int i = 0; i < activeRes.size(); i++) - { - int index = Integer.parseInt(activeRes.get(i).toString()); + if (!aa[activeRow].hasIcons) + { + aa[activeRow].hasIcons = true; + } - if (anot[index] == null) - { - anot[index] = new Annotation("", "", ' ', 0); + String label = JOptionPane.showInputDialog("Enter a label for the structure?", + symbol); + + 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 (anot[index] == null) + { + anot[index] = new Annotation(label, "", type, 0); + } + + anot[index].secondaryStructure = type; + anot[index].displayCharacter = label; + } } - anot[index].colour = col; - } + adjustPanelHeight(); + repaint(); + + return; } - 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"; - } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mousePressed(MouseEvent evt) + { - if (!aa[activeRow].hasIcons) - { - aa[activeRow].hasIcons = true; - } - String label = JOptionPane.showInputDialog( - "Enter a label for the structure?", - symbol); + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if(aa==null) + return; - if (label == null) - { - label = ""; - } - if ( (label.length() > 0) && !aa[activeRow].hasText) - { - aa[activeRow].hasText = true; - } + int height = 0; + activeRow = -1; - for (int i = 0; i < activeRes.size(); i++) - { - int index = Integer.parseInt(activeRes.get(i).toString()); - if (anot[index] == null) + for (int i = 0; i < aa.length; i++) { - anot[index] = new Annotation(label, "", type, 0); + if (aa[i].visible) + { + height += aa[i].height; + } + + if (evt.getY() < height) + { + if (aa[i].editable) + { + activeRow = i; + } + else if(aa[i].graph>0) + { + //Stretch Graph + graphStretch = i; + graphStretchY = evt.getY(); + } + + break; + } } - anot[index].secondaryStructure = type; - anot[index].displayCharacter = label; - } - } - adjustPanelHeight(); - activeRes = null; - repaint(); + if (SwingUtilities.isRightMouseButton(evt) && activeRow!=-1) + { + if (av.getColumnSelection() == null) + { + return; + } - return; - } + JPopupMenu pop = new JPopupMenu("Structure type"); + JMenuItem item = new JMenuItem(HELIX); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(SHEET); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(LABEL); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(COLOUR); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(REMOVE); + item.addActionListener(this); + pop.add(item); + pop.show(this, evt.getX(), evt.getY()); + + return; + } - public void mousePressed(MouseEvent evt) - { - int height = 0; - activeRow = -1; - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + if (aa == null) + { + return; + } - for (int i = 0; i < aa.length; i++) - { - height += aa[i].height; + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - if (evt.getY() < height) - { - if (aa[i].editable) - activeRow = i; - else - activeRes = null; + min = res; + max = res; - break; - } - } + if (av.getColumnSelection().contains(res)) + av.getColumnSelection().removeElement(res); + else + { + av.getColumnSelection().addElement(res); + SequenceGroup sg = new SequenceGroup(); + for (int i = 0; i < av.alignment.getSequences().size(); i++) + { + sg.addSequence(av.alignment.getSequenceAt(i), false); + } - if (SwingUtilities.isRightMouseButton(evt)) - { - if (activeRes == null) - { - return; - } + sg.setStartRes(res); + sg.setEndRes(res); + av.setSelectionGroup(sg); + } + ap.repaint(); - JPopupMenu pop = new JPopupMenu("Structure type"); - JMenuItem item = new JMenuItem(HELIX); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(SHEET); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(LABEL); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(COLOUR); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(REMOVE); - item.addActionListener(this); - pop.add(item); - pop.show(this, evt.getX(), evt.getY()); - - return; } - - if (aa == null) + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseReleased(MouseEvent evt) { - return; + graphStretch = -1; + graphStretchY = -1; + mouseDragging = false; } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseEntered(MouseEvent evt) + { + if(mouseDragging) + ap.seqPanel.scrollCanvas(null); + } - int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - - if (evt.isControlDown() || evt.isAltDown()) + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseExited(MouseEvent evt) { - addEditableColumn(res); + if(mouseDragging) + ap.seqPanel.scrollCanvas(evt); } - else if (evt.isShiftDown()) + + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseDragged(MouseEvent evt) { - if (activeRes == null) + if(graphStretch>-1) { - activeRes = new ArrayList(); + av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY(); + if(av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight <0) + av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0; + graphStretchY = evt.getY(); + adjustPanelHeight(); + ap.repaint(); } else { - int start = Integer.parseInt(activeRes.get(activeRes.size() - - 1).toString()); - int end = res; + mouseDragging = true; + + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + + SequenceGroup sg = av.getSelectionGroup(); - if (end < start) + if (res < min) { - int temp = end; - end = start; - start = temp; + min = res; } - for (int n = start; n <= end; n++) + if (res > max) { - addEditableColumn(n); + max = res; + } + + if (sg != null) + { + if (!av.getColumnSelection().contains(res)) + { + av.getColumnSelection().addElement(res); + } + + if (res > sg.getStartRes()) + { + sg.setEndRes(res); + } + else if (res < sg.getStartRes()) + { + sg.setStartRes(res); + } + + for (int i = min; i <= max; i++) + { + if ((i < sg.getStartRes()) || (i > sg.getEndRes())) + { + av.getColumnSelection().removeElement(i); + } + else + { + av.getColumnSelection().addElement(i); + } + } + + ap.repaint(); } + } } - else - { - activeRes = new ArrayList(); - activeRes.add(String.valueOf(res)); - } - repaint(); - } + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseMoved(MouseEvent evt) + { + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - public void mouseReleased(MouseEvent evt) - { - } + if (aa == null) + { + return; + } - public void mouseEntered(MouseEvent evt) - { - } + int row = -1; + int height = 0; - public void mouseExited(MouseEvent evt) - { - } + for (int i = 0; i < aa.length; i++) + { + if (aa[i].visible) + { + height += aa[i].height; + } - public void mouseDragged(MouseEvent evt) - { - } + if (evt.getY() < height) + { + row = i; - public void mouseMoved(MouseEvent evt) - { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + break; + } + } - if (aa == null) - { - return; - } + int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - int row = -1; - int height = 0; + if(av.hasHiddenColumns) + res = av.getColumnSelection().adjustForHiddenColumns(res); - for (int i = 0; i < aa.length; i++) - { - if (aa[i].visible) - { - height += aa[i].height; - } + if (row > -1 && res-1) + { + StringBuffer tip = new StringBuffer(""); + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[row].graphGroup && aa[gg].annotations[res]!=null) + tip.append(aa[gg].label+" "+aa[gg].annotations[res].description+"
" ); + } + if(tip.length()!=6) + { + tip.setLength(tip.length() - 4); + this.setToolTipText(tip.toString() + ""); + } + } + else if(aa[row].annotations[res] != null) + this.setToolTipText(aa[row].annotations[res].description); - if (evt.getY() < height) - { - row = i; + if(aa[row].annotations[res]!=null) + { + StringBuffer text = new StringBuffer("Sequence position " + + (res + 1) + " " + + aa[row].annotations[res].description); - break; - } + ap.alignFrame.statusBar.setText(text.toString()); + } + } } - int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void mouseClicked(MouseEvent evt) + { + } - if ( (row > -1) && (res < aa[row].annotations.length) && - (aa[row].annotations[res] != null)) + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + */ + public void paintComponent(Graphics g) { - this.setToolTipText(aa[row].annotations[res].description); + g.setColor(Color.white); + g.fillRect(0, 0, getWidth(), getHeight()); - StringBuffer text = new StringBuffer("Sequence position " + - (res + 1) + " " + - aa[row].annotations[res].description); - ap.alignFrame.statusBar.setText(text.toString()); - } - } + if(image!=null) + {if (fastPaint + || (getVisibleRect().width != g.getClipBounds().width) + || (getVisibleRect().height != g.getClipBounds().height)) + { + g.drawImage(image, 0, 0, this); + fastPaint = false; + return; + } + } + imgWidth = (av.endRes - av.startRes + 1) * av.charWidth; - public void mouseClicked(MouseEvent evt) - { - } + if (image == null || imgWidth != image.getWidth() + || image.getHeight(this) != getHeight()) + { + image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(), + BufferedImage.TYPE_INT_RGB); + gg = (Graphics2D) image.getGraphics(); + + if(av.antiAlias) + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + + gg.setFont(av.getFont()); + fm = gg.getFontMetrics(); + gg.setColor(Color.white); + gg.fillRect(0, 0, imgWidth, image.getHeight()); + } - public void paintComponent(Graphics g) - { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - if (fastPaint) - { + drawComponent(gg, av.startRes, av.endRes + 1); g.drawImage(image, 0, 0, this); - fastPaint = false; - - return; } - imgWidth = (av.endRes - av.startRes + 1) * av.charWidth; + /** + * DOCUMENT ME! + * + * @param horizontal DOCUMENT ME! + */ + public void fastPaint(int horizontal) + { + if ((horizontal == 0) + || gg==null + || av.alignment.getAlignmentAnnotation()==null + || av.alignment.getAlignmentAnnotation().length < 1 + || av.updatingConsensus + || av.updatingConservation) + { + repaint(); + return; + } + + gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0); - image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(), - BufferedImage.TYPE_INT_RGB); - gg = (Graphics2D) image.getGraphics(); - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + int sr = av.startRes; + int er = av.endRes + 1; + int transX = 0; - gg.setFont(av.getFont()); - fm = gg.getFontMetrics(); + 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; + } - drawComponent(gg, av.startRes, av.endRes + 1); - g.drawImage(image, 0, 0, this); - } + gg.translate(transX, 0); - public void fastPaint(int horizontal) - { - if ( (horizontal == 0) || - (av.alignment.getAlignmentAnnotation() == null) || - (av.alignment.getAlignmentAnnotation().length < 1)) - { - repaint(); + drawComponent(gg, sr, er); - return; - } + gg.translate(-transX, 0); - gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0); + fastPaint = true; - int sr = av.startRes; - int er = av.endRes + 1; - int transX = 0; + repaint(); - if (horizontal > 0) // scrollbar pulled right, image to the left - { - transX = (er - sr - horizontal) * av.charWidth; - sr = er - horizontal; } - else if (horizontal < 0) + + /** + * DOCUMENT ME! + * + * @param g DOCUMENT ME! + * @param startRes DOCUMENT ME! + * @param endRes DOCUMENT ME! + */ + public void drawComponent(Graphics g, int startRes, int endRes) { - er = sr - horizontal; - } + if(av.updatingConsensus || av.updatingConservation) + { + //We'll keep a record of the old image, + //and draw a faded image until the calculation + //has completed + if(fadedImage==null + || fadedImage.getWidth()!=imgWidth + || fadedImage.getHeight()!=image.getHeight()) + { + fadedImage = new BufferedImage( + imgWidth, image.getHeight(), + BufferedImage.TYPE_INT_RGB); + + Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics(); - gg.translate(transX, 0); + fadedG.setColor(Color.white); + fadedG.fillRect(0, 0, imgWidth, image.getHeight()); - drawComponent(gg, sr, er); + fadedG.setComposite( + AlphaComposite.getInstance( + AlphaComposite.SRC_OVER, .3f)); + fadedG.drawImage(image, 0, 0, this); - gg.translate( -transX, 0); + } - fastPaint = true; - repaint(); - } + } + else + fadedImage = null; - public void drawComponent(Graphics2D g, int startRes, int endRes) - { - g.setColor(Color.white); - g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight()); - if ( (av.alignment.getAlignmentAnnotation() == null) || - (av.alignment.getAlignmentAnnotation().length < 1)) - { g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - g.setColor(Color.black); - g.drawString("Alignment has no annotations", 20, 15); + g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight()); - return; - } + g.setFont(av.getFont()); + if (fm == null) + fm = g.getFontMetrics(); - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - int j; - int x = 0; - int y = 0; - char[] lastSS = new char[aa.length]; - int[] lastSSX = new int[aa.length]; - int iconOffset = av.charHeight / 2; - boolean validRes = false; - //\u03B2 \u03B1 - for (int i = 0; i < aa.length; i++) - { - AlignmentAnnotation row = aa[i]; - if (!row.visible) - { - continue; - } - - if (row.isGraph) - { - // this is so that we draw the characters below the graph - y += row.height; - - if (row.hasText) + if ( (av.alignment.getAlignmentAnnotation() == null) || + (av.alignment.getAlignmentAnnotation().length < 1)) { - y -= av.charHeight; + g.setColor(Color.white); + g.fillRect(0, 0, getWidth(), getHeight()); + g.setColor(Color.black); + if(av.validCharWidth) + g.drawString("Alignment has no annotations", 20, 15); + + return; } - } - if (row.hasText) - { - iconOffset = av.charHeight / 2; - } - else - { - iconOffset = 0; - } - for (j = startRes; j < endRes; j++) - { - if ( (row.annotations.length <= j) || - (row.annotations[j] == null)) - { - validRes = false; - } - else - { - validRes = true; - } + AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + + int x = 0, y = 0; + int column=0; + char lastSS; + int lastSSX; + int iconOffset = av.charHeight / 2; + boolean validRes = false; - x = (j - startRes) * av.charWidth; + boolean [] graphGroupDrawn = new boolean[aa.length]; - if (activeRow == i) + + //\u03B2 \u03B1 + for (int i = 0; i < aa.length; i++) { - g.setColor(Color.red); + AlignmentAnnotation row = aa[i]; - if (activeRes != null) - { - for (int n = 0; n < activeRes.size(); n++) + if (!row.visible) { - int v = Integer.parseInt(activeRes.get(n).toString()); - - if (v == j) - { - g.fillRect( (j - startRes) * av.charWidth, y, - av.charWidth, row.height); - } + continue; } - } - } - if (validRes && - (row.annotations[j].displayCharacter.length() > 0)) - { - int charOffset = (av.charWidth - - fm.charWidth(row.annotations[j].displayCharacter. - charAt( - 0))) / 2; - g.setColor(row.annotations[j].colour); - if (j == 0) - { - if ( (row.annotations[0].secondaryStructure == 'H') || - (row.annotations[0].secondaryStructure == 'E')) + lastSS = ' '; + lastSSX = 0; + + if (row.graph>0) { - g.drawString(row.annotations[j].displayCharacter, - x, y + iconOffset + 2); - } - } - else if ( ( (row.annotations[j].secondaryStructure == 'H') || - (row.annotations[j].secondaryStructure == 'E')) && - ( (row.annotations[j - 1] == null) || - (row.annotations[j].secondaryStructure != row.annotations[j - - 1].secondaryStructure))) - { - g.drawString(row.annotations[j].displayCharacter, x, - y + iconOffset + 2); - } + if(row.graphGroup>-1 && graphGroupDrawn[ row.graphGroup ] ) + continue; - if (!row.hasIcons) - { - g.drawString(row.annotations[j].displayCharacter, - x + charOffset, y + iconOffset + 2); - } - } + // this is so that we draw the characters below the graph + y += row.height; - if (row.hasIcons) - { - if (!validRes || - (row.annotations[j].secondaryStructure != lastSS[i])) - { - switch (lastSS[i]) + if (row.hasText) + { + y -= av.charHeight; + } + } + + if (av.updatingConsensus && aa[i].label.equals("Consensus")) { - case 'H': - g.setColor(HELIX_COLOUR); - g.fillRoundRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i], 7, 8, 8); + y += av.charHeight; - break; + g.drawImage(fadedImage, + 0,y-row.height,imgWidth, y, + 0,y-row.height,imgWidth, y, this); + g.setColor(Color.black); + // g.drawString("Calculating Consensus....",20, y-row.height/2); - case 'E': - g.setColor(SHEET_COLOUR); - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i] - 4, 7); - g.fillPolygon(new int[] - {x - 4, x - 4, x}, - new int[] - { - y + iconOffset, y + 14 + iconOffset, - y + 8 + iconOffset - }, 3); + continue; + } + else if (av.updatingConservation && aa[i].label.equals("Conservation")) + { - break; + y += av.charHeight; + g.drawImage(fadedImage, + 0, y - row.height, imgWidth, y, + 0, y - row.height, imgWidth, y, this); - case 'C': - break; + g.setColor(Color.black); + // g.drawString("Calculating Conservation.....",20, y-row.height/2); - default: - g.setColor(Color.gray); - g.fillRect(lastSSX[i], y + 6 + iconOffset, - x - lastSSX[i], 2); + continue; + } + else if (av.updatingConservation && aa[i].label.equals("Quality")) + { - break; + y += av.charHeight; + g.drawImage(fadedImage, + 0, y - row.height, imgWidth, y, + 0, y - row.height, imgWidth, y, this); + g.setColor(Color.black); + /// g.drawString("Calculating Quality....",20, y-row.height/2); + + continue; } - if (validRes) + + if (row.hasText) { - lastSS[i] = row.annotations[j].secondaryStructure; + iconOffset = av.charHeight / 2 + 4; } else { - lastSS[i] = ' '; + iconOffset = 0; } - lastSSX[i] = x; - } - } - - if (validRes && row.isGraph) - { - g.setColor(new Color(0, 0, 180)); + 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 ); + } + 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 ); + } + } + + 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++; + } - int height = (int) ( (row.annotations[j].value / row.graphMax) * - GRAPH_HEIGHT); + if(column>=row.annotations.length) + column = row.annotations.length-1; - if (row.windowLength > 1) - { - int total = 0; + // x ++; - for (int i2 = j - (row.windowLength / 2); - i2 < (j + (row.windowLength / 2)); i2++) + if (row.hasIcons) { - if ( (i2 < 0) || (i2 >= av.alignment.getWidth())) + switch (lastSS) { - continue; + 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+1) * 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; } + } - total += row.annotations[i2].value; + if (row.graph>0 && row.graphHeight>0) + { + if(row.graph == AlignmentAnnotation.LINE_GRAPH ) + { + if(row.graphGroup>-1 && !graphGroupDrawn[row.graphGroup]) + { + float groupmax=-999999, groupmin=9999999; + for(int gg=0; gggroupmax) + groupmax = aa[gg].graphMax; + if(aa[gg].graphMin0 && row.hasText) + { + y += av.charHeight; + } - g.setColor(row.annotations[j].colour); - g.fillRect(x, y - height, av.charWidth, height); + 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 aaMax) + { + break; + } - case 'E': - g.setColor(SHEET_COLOUR); - g.fillRect(lastSSX[i], y + 4 + iconOffset, - x - lastSSX[i] - 4, 7); - g.fillPolygon(new int[] - {x - 4, x - 4, x}, - new int[] - { - y + iconOffset, y + 14 + iconOffset, - y + 7 + iconOffset - }, 3); + if(aa.annotations[column]==null || aa.annotations[column-1]==null) + { + x++; + continue; + } - break; - case 'C': - break; + 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); - default: - g.setColor(Color.gray); - g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2); + g.drawLine(x*av.charWidth-av.charWidth/2, y1, x*av.charWidth+av.charWidth/2, y2); + x ++; + } - break; - } + if(aa.threshold!=null) + { + g.setColor(aa.threshold.colour); + Graphics2D g2 = (Graphics2D)g; + g2.setStroke(new BasicStroke(1, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, 3f, + new float[] { 5f, 3f }, 0f)); + + y2 = (int)(y - ((aa.threshold.value-min) / range)*graphHeight); + g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2); + g2.setStroke(new BasicStroke()); } + } + + 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; - if (row.isGraph && row.hasText) + 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 ) { - y += av.charHeight; - } + column = sRes + x; + if(av.hasHiddenColumns) + { + column = av.getColumnSelection().adjustForHiddenColumns(column); + } - if (!row.isGraph) + 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) { - y += aa[i].height; + g.setColor(aa.threshold.colour); + Graphics2D g2 = (Graphics2D)g; + g2.setStroke(new BasicStroke(1, + BasicStroke.CAP_SQUARE, + BasicStroke.JOIN_ROUND, 3f, + new float[] { 5f, 3f }, 0f)); + + y2 = (int)(y - ((aa.threshold.value-min) / range)*aa.graphHeight); + g.drawLine(0,y2,(eRes-sRes)*av.charWidth,y2); + g2.setStroke(new BasicStroke()); } } - } - - // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y) - { - g.setColor(Color.white); - g.fillRect(0, 0, width, y); - g.setColor(new Color(0, 0, 180)); - - int x = 0; - for (int j = 0; j < aa.annotations.length; j++) + // 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 height = (int) ( (aa.annotations[j].value / aa.graphMax) * - GRAPH_HEIGHT); - g.fillRect(x, y - height, av.charWidth, height); - x += av.charWidth; + int x = 0, height; + + for (int j = sRes; j < eRes; j++) + { + if (aa.annotations[j] != null) + { + g.setColor(aa.annotations[j].colour); + + height = (int) ( (aa.annotations[j].value / aa.graphMax) * y); + if (height > y) + height = y; + + g.fillRect(x, y - height, av.charWidth, height); + } + x += av.charWidth; + } } - } + }