X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=8a222884824b30fa14c8d586e0fa664fb9f7e8da;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=755b85a1888eeb41bba73b90b44de3f7a217180c;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 755b85a..8a22288 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -1,74 +1,80 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.awt.*; import java.awt.event.*; -import java.awt.font.LineMetrics; -import java.awt.geom.AffineTransform; import java.awt.image.*; -import java.util.Hashtable; - import javax.swing.*; -import jalview.analysis.AAFrequency; import jalview.datamodel.*; -import jalview.schemes.ColourSchemeI; +import jalview.renderer.AnnotationRenderer; +import jalview.renderer.AwtRenderPanelI; /** - * DOCUMENT ME! + * AnnotationPanel displays visible portion of annotation rows below unwrapped + * alignment * * @author $author$ * @version $Revision$ */ -public class AnnotationPanel extends JPanel implements MouseListener, - MouseMotionListener, ActionListener, AdjustmentListener +public class AnnotationPanel extends JPanel implements AwtRenderPanelI, + MouseListener, MouseWheelListener, MouseMotionListener, + ActionListener, AdjustmentListener, Scrollable { 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(); + public final Color HELIX_COLOUR = Color.red.darker(); + + public final Color SHEET_COLOUR = Color.green.darker().darker(); - final Color SHEET_COLOUR = Color.green.darker().darker(); + public final Color STEM_COLOUR = Color.blue.darker(); /** DOCUMENT ME!! */ - AlignViewport av; + public AlignViewport av; AlignmentPanel ap; - int activeRow = -1; + public int activeRow = -1; - BufferedImage image; + public BufferedImage image; - BufferedImage fadedImage; + public volatile BufferedImage fadedImage; Graphics2D gg; - FontMetrics fm; + public FontMetrics fm; - int imgWidth = 0; + public int imgWidth = 0; boolean fastPaint = false; @@ -85,6 +91,15 @@ public class AnnotationPanel extends JPanel implements MouseListener, boolean MAC = false; + // for editing cursor + int cursorX = 0; + + int cursorY = 0; + + public final AnnotationRenderer renderer; + + private MouseWheelListener[] _mwl; + /** * Creates a new AnnotationPanel object. * @@ -106,21 +121,96 @@ public class AnnotationPanel extends JPanel implements MouseListener, addMouseMotionListener(this); ap.annotationScroller.getVerticalScrollBar() .addAdjustmentListener(this); + // save any wheel listeners on the scroller, so we can propagate scroll + // events to them. + _mwl = ap.annotationScroller.getMouseWheelListeners(); + // and then set our own listener to consume all mousewheel events + ap.annotationScroller.addMouseWheelListener(this); + renderer = new AnnotationRenderer(); } public AnnotationPanel(AlignViewport av) { this.av = av; + renderer = new AnnotationRenderer(); } - /** - * DOCUMENT ME! + @Override + public void mouseWheelMoved(MouseWheelEvent e) + { + if (e.isShiftDown()) + { + e.consume(); + if (e.getWheelRotation() > 0) + { + ap.scrollRight(true); + } + else + { + ap.scrollRight(false); + } + } + else + { + // TODO: find the correct way to let the event bubble up to + // ap.annotationScroller + for (MouseWheelListener mwl : _mwl) + { + if (mwl != null) + { + mwl.mouseWheelMoved(e); + } + if (e.isConsumed()) + { + break; + } + } + } + } + + @Override + public Dimension getPreferredScrollableViewportSize() + { + return getPreferredSize(); + } + + @Override + public int getScrollableBlockIncrement(Rectangle visibleRect, + int orientation, int direction) + { + return 30; + } + + @Override + public boolean getScrollableTracksViewportHeight() + { + return false; + } + + @Override + public boolean getScrollableTracksViewportWidth() + { + return true; + } + + @Override + public int getScrollableUnitIncrement(Rectangle visibleRect, + int orientation, int direction) + { + return 30; + } + + /* + * (non-Javadoc) * - * @param evt - * DOCUMENT ME! + * @see + * java.awt.event.AdjustmentListener#adjustmentValueChanged(java.awt.event + * .AdjustmentEvent) */ + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { + // update annotation label display ap.alabels.setScrollOffset(-evt.getValue()); } @@ -132,54 +222,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ 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] == null) - { - System.err.println("Null annotation row: ignoring."); - continue; - } - 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; - } - + int height = av.calcPanelHeight(); this.setPreferredSize(new Dimension(1, height)); if (ap != null) { @@ -196,9 +239,14 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void actionPerformed(ActionEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); + if (aa == null) + { + return; + } Annotation[] anot = aa[activeRow].annotations; if (anot.length < av.getColumnSelection().getMax()) @@ -236,7 +284,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, { int index = av.getColumnSelection().columnAt(i); - if (!av.colSel.isVisible(index)) + if (!av.getColumnSelection().isVisible(index)) continue; if (anot[index] == null) @@ -261,7 +309,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, { int index = av.getColumnSelection().columnAt(i); - if (!av.colSel.isVisible(index)) + if (!av.getColumnSelection().isVisible(index)) continue; if (anot[index] == null) @@ -288,6 +336,13 @@ public class AnnotationPanel extends JPanel implements MouseListener, symbol = "\u03B2"; } + // Added by LML to color stems + else if (evt.getActionCommand().equals(STEM)) + { + type = 'S'; + symbol = "\u03C3"; + } + if (!aa[activeRow].hasIcons) { aa[activeRow].hasIcons = true; @@ -310,7 +365,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, { int index = av.getColumnSelection().columnAt(i); - if (!av.colSel.isVisible(index)) + if (!av.getColumnSelection().isVisible(index)) continue; if (anot[index] == null) @@ -322,7 +377,9 @@ public class AnnotationPanel extends JPanel implements MouseListener, anot[index].displayCharacter = label; } } - + av.getAlignment().validateAnnotation(aa[activeRow]); + ap.alignmentChanged(); + adjustPanelHeight(); repaint(); @@ -334,22 +391,25 @@ public class AnnotationPanel extends JPanel implements MouseListener, { String collatedInput = ""; String last = ""; + ColumnSelection viscols = av.getColumnSelection(); + // TODO: refactor and save av.getColumnSelection for efficiency for (int i = 0; i < columnSelection.size(); i++) { int index = columnSelection.columnAt(i); // always check for current display state - just in case - if (!av.colSel.isVisible(index)) + if (!viscols.isVisible(index)) continue; String tlabel = null; if (anot[index] != null) - { + { // LML added stem code if (label2.equals(HELIX) || label2.equals(SHEET) - || label2.equals(LABEL)) + || label2.equals(STEM) || label2.equals(LABEL)) { tlabel = anot[index].description; if (tlabel == null || tlabel.length() < 1) { - if (label2.equals(HELIX) || label2.equals(SHEET)) + if (label2.equals(HELIX) || label2.equals(SHEET) + || label2.equals(STEM)) { tlabel = "" + anot[index].secondaryStructure; } @@ -378,10 +438,11 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { return; @@ -422,12 +483,25 @@ public class AnnotationPanel extends JPanel implements MouseListener, } 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); + JMenuItem item; + /* + * Just display the needed structure options + */ + if (av.getAlignment().isNucleotide() == true) + { + item = new JMenuItem(STEM); + item.addActionListener(this); + pop.add(item); + } + else + { + 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); @@ -457,6 +531,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent evt) { graphStretch = -1; @@ -471,6 +546,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent evt) { ap.scalePanel.mouseEntered(evt); @@ -482,6 +558,7 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent evt) { ap.scalePanel.mouseExited(evt); @@ -493,15 +570,16 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent evt) { if (graphStretch > -1) { - av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY + av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY - evt.getY(); - if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0) + if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0) { - av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0; + av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0; } graphStretchY = evt.getY(); adjustPanelHeight(); @@ -519,9 +597,10 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseMoved(MouseEvent evt) { - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); if (aa == null) { @@ -555,13 +634,13 @@ public class AnnotationPanel extends JPanel implements MouseListener, int res = (evt.getX() / av.getCharWidth()) + av.getStartRes(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { res = av.getColumnSelection().adjustForHiddenColumns(res); } if (row > -1 && aa[row].annotations != null - && res < (int) aa[row].annotations.length) + && res < aa[row].annotations.length) { if (aa[row].graphGroup > -1) { @@ -618,16 +697,47 @@ public class AnnotationPanel extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseClicked(MouseEvent evt) { +// if (activeRow != -1) +// { +// AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); +// AlignmentAnnotation anot = aa[activeRow]; +// } } + // TODO mouseClicked-content and drawCursor are quite experimental! + public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1, + int y1) + { + int pady = av.charHeight / 5; + int charOffset = 0; + graphics.setColor(Color.black); + graphics.fillRect(x1, y1, av.charWidth, av.charHeight); + + if (av.validCharWidth) + { + graphics.setColor(Color.white); + + char s = seq.getCharAt(res); + + charOffset = (av.charWidth - fm.charWidth(s)) / 2; + graphics.drawString(String.valueOf(s), charOffset + x1, + (y1 + av.charHeight) - pady); + } + + } + + private volatile boolean imageFresh = false; + /** * DOCUMENT ME! * * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { g.setColor(Color.white); @@ -646,11 +756,27 @@ public class AnnotationPanel extends JPanel implements MouseListener, imgWidth = (av.endRes - av.startRes + 1) * av.charWidth; if (imgWidth < 1) return; - if (image == null || imgWidth != image.getWidth() + if (image == null || imgWidth != image.getWidth(this) || image.getHeight(this) != getHeight()) { - image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(), - BufferedImage.TYPE_INT_RGB); + try + { + image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(), + BufferedImage.TYPE_INT_RGB); + } catch (OutOfMemoryError oom) + { + try + { + System.gc(); + } catch (Exception x) + { + } + ; + new OOMWarning( + "Couldn't allocate memory to redraw screen. Please restart Jalview", + oom); + return; + } gg = (Graphics2D) image.getGraphics(); if (av.antiAlias) @@ -663,12 +789,17 @@ public class AnnotationPanel extends JPanel implements MouseListener, fm = gg.getFontMetrics(); gg.setColor(Color.white); gg.fillRect(0, 0, imgWidth, image.getHeight()); + imageFresh = true; } drawComponent(gg, av.startRes, av.endRes + 1); + imageFresh = false; g.drawImage(image, 0, 0, this); } - + /** + * set true to enable redraw timing debug output on stderr + */ + private final boolean debugRedraw = false; /** * non-Thread safe repaint * @@ -677,17 +808,17 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void fastPaint(int horizontal) { - if ((horizontal == 0) || gg == null - || av.alignment.getAlignmentAnnotation() == null - || av.alignment.getAlignmentAnnotation().length < 1 - || av.updatingConsensus || av.updatingConservation) + || av.getAlignment().getAlignmentAnnotation() == null + || av.getAlignment().getAlignmentAnnotation().length < 1 + || av.isCalcInProgress()) { repaint(); return; } + long stime=System.currentTimeMillis(); gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0); - + long mtime=System.currentTimeMillis(); int sr = av.startRes; int er = av.endRes + 1; int transX = 0; @@ -707,12 +838,18 @@ public class AnnotationPanel extends JPanel implements MouseListener, drawComponent(gg, sr, er); gg.translate(-transX, 0); - + long dtime=System.currentTimeMillis(); fastPaint = true; repaint(); + long rtime=System.currentTimeMillis(); + if (debugRedraw) { + System.err.println("Scroll:\t"+horizontal+"\tCopyArea:\t"+(mtime-stime)+"\tDraw component:\t"+(dtime-mtime)+"\tRepaint call:\t"+(rtime-dtime)); + } } + private volatile boolean lastImageGood = false; + /** * DOCUMENT ME! * @@ -725,18 +862,23 @@ public class AnnotationPanel extends JPanel implements MouseListener, */ public void drawComponent(Graphics g, int startRes, int endRes) { - if (av.updatingConsensus || av.updatingConservation) + BufferedImage oldFaded = fadedImage; + if (av.isCalcInProgress()) { if (image == null) { + lastImageGood = false; return; } // 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()) + if (lastImageGood + && (fadedImage == null || fadedImage.getWidth() != imgWidth || fadedImage + .getHeight() != image.getHeight())) { + // System.err.println("redraw faded image ("+(fadedImage==null ? + // "null image" : "") + " lastGood="+lastImageGood+")"); fadedImage = new BufferedImage(imgWidth, image.getHeight(), BufferedImage.TYPE_INT_RGB); @@ -750,13 +892,20 @@ public class AnnotationPanel extends JPanel implements MouseListener, fadedG.drawImage(image, 0, 0, this); } + // make sure we don't overwrite the last good faded image until all + // calculations have finished + lastImageGood = false; } else { + if (fadedImage != null) + { + oldFaded = fadedImage; + } fadedImage = null; } - + g.setColor(Color.white); g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight()); @@ -766,8 +915,8 @@ public class AnnotationPanel extends JPanel implements MouseListener, fm = g.getFontMetrics(); } - if ((av.alignment.getAlignmentAnnotation() == null) - || (av.alignment.getAlignmentAnnotation().length < 1)) + if ((av.getAlignment().getAlignmentAnnotation() == null) + || (av.getAlignment().getAlignmentAnnotation().length < 1)) { g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); @@ -779,714 +928,41 @@ public class AnnotationPanel extends JPanel implements MouseListener, return; } - - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); - - int x = 0, y = 0; - int column = 0; - char lastSS; - int lastSSX; - int iconOffset = 0; - boolean validRes = false; - boolean validEnd = false; - boolean labelAllCols = false; - boolean centreColLabels, centreColLabelsDef = av - .getCentreColumnLabels(); - boolean scaleColLabel = false; - boolean[] graphGroupDrawn = new boolean[aa.length]; - int charOffset = 0; // offset for a label - float fmWidth, fmScaling = 1f; // scaling for a label to fit it into a - // column. - Font ofont = g.getFont(); - // \u03B2 \u03B1 - for (int i = 0; i < aa.length; i++) + lastImageGood = renderer.drawComponent(this, av, g, activeRow, + startRes, endRes); + if (!lastImageGood && fadedImage == null) { - AlignmentAnnotation row = aa[i]; - - if (!row.visible) - { - continue; - } - centreColLabels = row.centreColLabels || centreColLabelsDef; - labelAllCols = row.showAllColLabels; - scaleColLabel = row.scaleColLabel; - 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) - { - iconOffset = av.charHeight - fm.getDescent(); - y -= av.charHeight; - } - } - else if (row.hasText) - { - iconOffset = av.charHeight - fm.getDescent(); - - } - else - { - iconOffset = 0; - } - - if (av.updatingConsensus && aa[i] == av.consensus) - { - 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 Consensus....",20, y-row.height/2); - - continue; - } - else if (av.updatingConservation - && aa[i].label.equals("Conservation")) - { - - 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 Conservation.....",20, y-row.height/2); - - continue; - } - else if (av.updatingConservation && aa[i].label.equals("Quality")) - { - - 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; - } - - 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 == null) || (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)) - { - - if (centreColLabels || scaleColLabel) - { - fmWidth = (float) fm.charsWidth( - row.annotations[column].displayCharacter.toCharArray(), - 0, row.annotations[column].displayCharacter.length()); - - if (scaleColLabel) - { - // justify the label and scale to fit in column - if (fmWidth > av.charWidth) - { - // scale only if the current font isn't already small enough - fmScaling = av.charWidth; - fmScaling /= fmWidth; - g.setFont(ofont.deriveFont(AffineTransform - .getScaleInstance(fmScaling, 1.0))); - // and update the label's width to reflect the scaling. - fmWidth = av.charWidth; - } - } - } - else - { - fmWidth = (float) fm - .charWidth(row.annotations[column].displayCharacter - .charAt(0)); - } - charOffset = (int) ((av.charWidth - fmWidth) / 2f); - - 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); - } - else if (row.annotations[column - 1] == null - || (labelAllCols - || !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); - } - g.setFont(ofont); - } - - 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 (!validRes || 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 + 1) * av.charWidth - - lastSSX, 7); - } - break; - - default: - g.setColor(Color.gray); - g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth) - - lastSSX, 2); - - break; - } - } - - 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; 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; - } + fadedImage = oldFaded; } } - public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes, - int eRes, int y, float min, float max, int graphHeight) + @Override + public FontMetrics getFontMetrics() { - if (sRes > aa.annotations.length) - { - return; - } - - int x = 0; - - // Adjustment for fastpaint to left - if (eRes < av.endRes) - { - eRes++; - } - - eRes = Math.min(eRes, aa.annotations.length); - - if (sRes == 0) - { - x++; - } - - 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 + 1) * 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; - } - - if (aa.annotations[column].colour == null) - g.setColor(Color.black); - else - 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); - 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()); - } + return fm; } - public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes, - int eRes, float min, float max, int y) + @Override + public Image getFadedImage() { - ColourSchemeI profcolour = av.getGlobalColourScheme(); - if (profcolour == null) - { - profcolour = new jalview.schemes.ZappoColourScheme(); - } - if (sRes > aa.annotations.length) - { - return; - } - Font ofont = g.getFont(); - 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; - boolean renderHistogram = true, renderProfile = true; - if (aa.autoCalculated && aa.label.startsWith("Consensus")) - { - // TODO: generalise this to have render styles for consensus/profile data - if (aa.groupRef != null) - { - renderHistogram = aa.groupRef.isShowConsensusHistogram(); - renderProfile = aa.groupRef.isShowSequenceLogo(); - } - else - { - renderHistogram = av.isShowConsensusHistogram(); - renderProfile = av.isShowSequenceLogo(); - } - } - 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 (renderHistogram) - { - 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); - } - } - // draw profile if available - if (aa.annotations[column].value != 0 && renderProfile) - { - int profl[] = getProfileFor(aa, column); - int ht = y1, htn = y2 - y1;// aa.graphHeight; - float wdth; - double ht2 = 0; - char[] dc = new char[1]; - LineMetrics lm; - for (int c = 1; profl != null && c < profl[0];) - { - dc[0] = (char) profl[c++]; - wdth = av.charWidth; - wdth /= (float) fm.charsWidth(dc, 0, 1); - - if (c > 2) - { - ht += (int) ht2; - } - { - // if (aa.annotations[column].value==0) { - // g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, - // (ht2=(aa.graphHeight*0.1/av.charHeight))))); - // ht = y2-(int)ht2; - // } else { - g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance( - wdth, (ht2 = (htn * ((double) profl[c++]) / 100.0)) - / av.charHeight))); - lm = g.getFontMetrics().getLineMetrics(dc, 0, 1, g); - // htn -=ht2; - // } - g.setColor(profcolour.findColour(dc[0])); // (av.globalColourScheme!=null) - // ? );// try to get a - // colourscheme for the - // group(aa.groupRef.cs==null) - // ? av.textColour2 : - // cs.findColour(dc)); - g.drawChars(dc, 0, 1, x * av.charWidth, (int) (ht + lm - .getHeight())); - // ht+=g.getFontMetrics().getAscent()-g.getFontMetrics().getDescent(); - } - } - g.setFont(ofont); - } - x++; - } - 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) * aa.graphHeight); - g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2); - g2.setStroke(new BasicStroke()); - } + return fadedImage; } - private int[] getProfileFor(AlignmentAnnotation aa, int column) + @Override + public int getFadedImageWidth() { - if (aa.autoCalculated && aa.label.startsWith("Consensus")) - { - if (aa.groupRef != null && aa.groupRef.consensusData != null - && aa.groupRef.isShowSequenceLogo()) - { - return AAFrequency.extractProfile( - aa.groupRef.consensusData[column], aa.groupRef - .getIgnoreGapsConsensus()); - } - // TODO extend annotation row to enable dynamic and static profile data to - // be stored - if (aa.groupRef == null && aa.sequenceRef == null - && av.isShowSequenceLogo()) - { - return AAFrequency.extractProfile(av.hconsensus[column], av - .getIgnoreGapsConsensus()); - } - } - return null; + return imgWidth; } - - // used by overview window - public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, - int y, int sRes, int eRes) + private int[] bounds = new int[2]; + @Override + public int[] getVisibleVRange() { - 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 (ap!=null && ap.alabels!=null) { - if (aa.annotations[j] != null) - { - 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) * y); - if (height > y) - { - height = y; - } - - g.fillRect(x, y - height, av.charWidth, height); - } - x += av.charWidth; - } + int sOffset=-ap.alabels.scrollOffset; + int visHeight = sOffset+ap.annotationSpaceFillerHolder.getHeight(); + bounds[0] = sOffset; bounds[1]=visHeight; + return bounds; + } else return null; } - }