X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=a88aa4a4ee30b6e5ea5920c84140c92bd5af46dc;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=487b83279cc05c959cf0ab2d64af9a0ef84c7a11;hpb=7c69a7becdaa610db196fac609d978b165a801f2;p=jalview.git
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 487b832..a88aa4a 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,80 +1,115 @@
/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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 .
*/
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 com.stevesoft.pat.Regex;
+
+import jalview.analysis.AAFrequency;
+import jalview.analysis.StructureFrequency;
import jalview.datamodel.*;
+import jalview.schemes.ColourSchemeI;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class AnnotationPanel
- extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener, AdjustmentListener
+public class AnnotationPanel extends JPanel implements MouseListener,
+ MouseMotionListener, ActionListener, AdjustmentListener
{
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();
+ final Color STEM_COLOUR = Color.blue.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
+ // 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
+
+ int min; // used by mouseDragged to see if user
+
+ int max; // used by mouseDragged to see if user
+
boolean mouseDragging = false;
boolean MAC = false;
+ // for editing cursor
+ int cursorX = 0;
+
+ int cursorY = 0;
+
/**
* Creates a new AnnotationPanel object.
- *
- * @param ap DOCUMENT ME!
+ *
+ * @param ap
+ * DOCUMENT ME!
*/
public AnnotationPanel(AlignmentPanel ap)
{
- if (System.getProperty("os.name").startsWith("Mac"))
- {
- MAC = true;
- }
+ MAC = new jalview.util.Platform().isAMac();
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
@@ -84,7 +119,8 @@ public class AnnotationPanel
this.setLayout(null);
addMouseListener(this);
addMouseMotionListener(this);
- ap.annotationScroller.getVerticalScrollBar().addAdjustmentListener(this);
+ ap.annotationScroller.getVerticalScrollBar()
+ .addAdjustmentListener(this);
}
public AnnotationPanel(AlignViewport av)
@@ -94,19 +130,42 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- ap.alabels.setScrollOffset( -evt.getValue());
+ ap.alabels.setScrollOffset(-evt.getValue());
}
/**
- * DOCUMENT ME!
+ * Calculates the height of the annotation displayed in the annotation panel.
+ * Callers should normally call the ap.adjustAnnotationHeight method to ensure
+ * all annotation associated components are updated correctly.
+ *
*/
public int adjustPanelHeight()
{
+ int height = calcPanelHeight();
+ this.setPreferredSize(new Dimension(1, height));
+ if (ap != null)
+ {
+ // revalidate only when the alignment panel is fully constructed
+ ap.validate();
+ }
+
+ return height;
+ }
+
+ /**
+ * calculate the height for visible annotation, revalidating bounds where
+ * necessary ABSTRACT GUI METHOD
+ *
+ * @return total height of annotation
+ */
+ public int calcPanelHeight()
+ {
// setHeight of panels
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
int height = 0;
@@ -115,6 +174,11 @@ public class AnnotationPanel
{
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;
@@ -145,24 +209,27 @@ public class AnnotationPanel
height += aa[i].height;
}
}
- else
+ if (height == 0)
{
+ // set minimum
height = 20;
}
-
- this.setPreferredSize(new Dimension(1, height));
-
return height;
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
Annotation[] anot = aa[activeRow].annotations;
if (anot.length < av.getColumnSelection().getMax())
@@ -182,16 +249,16 @@ public class AnnotationPanel
}
else if (evt.getActionCommand().equals(LABEL))
{
- String label = JOptionPane.showInputDialog(this, "Enter Label ",
- "Enter label",
- JOptionPane.QUESTION_MESSAGE);
+ String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL);
+ String label = JOptionPane.showInputDialog(this, "Enter label",
+ exMesg);
if (label == null)
{
return;
}
- if ( (label.length() > 0) && !aa[activeRow].hasText)
+ if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
}
@@ -200,28 +267,32 @@ public class AnnotationPanel
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.colSel.isVisible(index))
continue;
if (anot[index] == null)
{
- anot[index] = new Annotation(label, "", ' ', 0);
+ anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
+ // null exceptions
+ // aren't raised
+ // elsewhere.
+ }
+ else
+ {
+ anot[index].displayCharacter = label;
}
-
- anot[index].displayCharacter = label;
}
}
else if (evt.getActionCommand().equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
- "Choose foreground colour",
- Color.black);
+ "Choose foreground colour", Color.black);
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.colSel.isVisible(index))
continue;
if (anot[index] == null)
@@ -232,7 +303,8 @@ public class AnnotationPanel
anot[index].colour = col;
}
}
- else // HELIX OR SHEET
+ else
+ // HELIX OR SHEET
{
char type = 0;
String symbol = "\u03B1";
@@ -247,21 +319,27 @@ public class AnnotationPanel
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;
}
String label = JOptionPane.showInputDialog(
- "Enter a label for the structure?",
- symbol);
+ "Enter a label for the structure?", symbol);
if (label == null)
{
return;
}
- if ( (label.length() > 0) && !aa[activeRow].hasText)
+ if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
}
@@ -270,7 +348,7 @@ public class AnnotationPanel
{
int index = av.getColumnSelection().columnAt(i);
- if(!av.colSel.isVisible(index))
+ if (!av.colSel.isVisible(index))
continue;
if (anot[index] == null)
@@ -289,10 +367,55 @@ public class AnnotationPanel
return;
}
+ private String collectAnnotVals(Annotation[] anot,
+ ColumnSelection columnSelection, String label2)
+ {
+ String collatedInput = "";
+ String last = "";
+ 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))
+ continue;
+ String tlabel = null;
+ if (anot[index] != null)
+ { // LML added stem code
+ if (label2.equals(HELIX) || label2.equals(SHEET)
+ || label2.equals(STEM) || label2.equals(LABEL))
+ {
+ tlabel = anot[index].description;
+ if (tlabel == null || tlabel.length() < 1)
+ {
+ if (label2.equals(HELIX) || label2.equals(SHEET)
+ || label2.equals(STEM))
+ {
+ tlabel = "" + anot[index].secondaryStructure;
+ }
+ else
+ {
+ tlabel = "" + anot[index].displayCharacter;
+ }
+ }
+ }
+ if (tlabel != null && !tlabel.equals(last))
+ {
+ if (last.length() > 0)
+ {
+ collatedInput += " ";
+ }
+ collatedInput += tlabel;
+ }
+ }
+ }
+ return collatedInput;
+ }
+
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
@@ -321,7 +444,7 @@ public class AnnotationPanel
}
else if (aa[i].graph > 0)
{
- //Stretch Graph
+ // Stretch Graph
graphStretch = i;
graphStretchY = evt.getY();
}
@@ -338,12 +461,25 @@ public class AnnotationPanel
}
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.alignment.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);
@@ -369,8 +505,9 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
@@ -382,18 +519,20 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent evt)
{
- ap.scalePanel.mouseEntered(evt);
+ ap.scalePanel.mouseEntered(evt);
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent evt)
{
@@ -402,15 +541,16 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
if (graphStretch > -1)
{
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight +=
- graphStretchY - evt.getY();
+ av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ - evt.getY();
if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)
{
av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
@@ -427,8 +567,9 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
@@ -471,19 +612,19 @@ public class AnnotationPanel
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
- if (aa[row].annotations != null
- && row > -1
- && res < (int) aa[row].annotations.length)
+ if (row > -1 && aa[row].annotations != null
+ && res < (int) aa[row].annotations.length)
{
if (aa[row].graphGroup > -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)
+ if (aa[gg].graphGroup == aa[row].graphGroup
+ && aa[gg].annotations[res] != null)
{
- tip.append(aa[gg].label + " " + aa[gg].annotations[res].description +
- "
");
+ tip.append(aa[gg].label + " "
+ + aa[gg].annotations[res].description + "
");
}
}
if (tip.length() != 6)
@@ -493,15 +634,21 @@ public class AnnotationPanel
}
}
else if (aa[row].annotations[res] != null
- && aa[row].annotations[res].description != null)
+ && aa[row].annotations[res].description != null
+ && aa[row].annotations[res].description.length() > 0)
{
this.setToolTipText(aa[row].annotations[res].description);
}
+ else
+ {
+ // clear the tooltip.
+ this.setToolTipText(null);
+ }
if (aa[row].annotations[res] != null)
{
- StringBuffer text = new StringBuffer("Sequence position " +
- (res + 1));
+ StringBuffer text = new StringBuffer("Sequence position "
+ + (res + 1));
if (aa[row].annotations[res].description != null)
{
@@ -519,17 +666,51 @@ public class AnnotationPanel
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
+ if (activeRow != -1)
+ {
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation anot = aa[activeRow];
+
+ if (anot.description.equals("secondary structure"))
+ {
+ // System.out.println(anot.description+" "+anot.getRNAStruc());
+ }
+ }
+ }
+
+ // 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);
+ }
+
}
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
@@ -538,9 +719,8 @@ public class AnnotationPanel
if (image != null)
{
- if (fastPaint
- || (getVisibleRect().width != g.getClipBounds().width)
- || (getVisibleRect().height != g.getClipBounds().height))
+ if (fastPaint || (getVisibleRect().width != g.getClipBounds().width)
+ || (getVisibleRect().height != g.getClipBounds().height))
{
g.drawImage(image, 0, 0, this);
fastPaint = false;
@@ -548,18 +728,19 @@ public class AnnotationPanel
}
}
imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
-
+ if (imgWidth < 1)
+ return;
if (image == null || imgWidth != image.getWidth()
- || image.getHeight(this) != getHeight())
+ || image.getHeight(this) != getHeight())
{
image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
- BufferedImage.TYPE_INT_RGB);
+ BufferedImage.TYPE_INT_RGB);
gg = (Graphics2D) image.getGraphics();
if (av.antiAlias)
{
gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ RenderingHints.VALUE_ANTIALIAS_ON);
}
gg.setFont(av.getFont());
@@ -573,23 +754,22 @@ public class AnnotationPanel
}
/**
- * DOCUMENT ME!
- *
- * @param horizontal DOCUMENT ME!
+ * non-Thread safe repaint
+ *
+ * @param horizontal
+ * repaint with horizontal shift in alignment
*/
public void fastPaint(int horizontal)
{
- if ( (horizontal == 0)
- || gg == null
- || av.alignment.getAlignmentAnnotation() == null
- || av.alignment.getAlignmentAnnotation().length < 1
- || av.updatingConsensus
- || av.updatingConservation)
+
+ 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);
int sr = av.startRes;
@@ -610,20 +790,22 @@ public class AnnotationPanel
drawComponent(gg, sr, er);
- gg.translate( -transX, 0);
+ gg.translate(-transX, 0);
fastPaint = true;
-
repaint();
}
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startRes DOCUMENT ME!
- * @param endRes DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
*/
public void drawComponent(Graphics g, int startRes, int endRes)
{
@@ -633,24 +815,21 @@ public class AnnotationPanel
{
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())
+ // 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);
+ fadedImage = new BufferedImage(imgWidth, image.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
Graphics2D fadedG = (Graphics2D) fadedImage.getGraphics();
fadedG.setColor(Color.white);
fadedG.fillRect(0, 0, imgWidth, image.getHeight());
- fadedG.setComposite(
- AlphaComposite.getInstance(
+ fadedG.setComposite(AlphaComposite.getInstance(
AlphaComposite.SRC_OVER, .3f));
fadedG.drawImage(image, 0, 0, this);
@@ -671,8 +850,8 @@ public class AnnotationPanel
fm = g.getFontMetrics();
}
- if ( (av.alignment.getAlignmentAnnotation() == null) ||
- (av.alignment.getAlignmentAnnotation().length < 1))
+ if ((av.alignment.getAlignmentAnnotation() == null)
+ || (av.alignment.getAlignmentAnnotation().length < 1))
{
g.setColor(Color.white);
g.fillRect(0, 0, getWidth(), getHeight());
@@ -687,16 +866,23 @@ public class AnnotationPanel
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- int x = 0, y=0;
+ 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];
-
- //\u03B2 \u03B1
+ 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++)
{
AlignmentAnnotation row = aa[i];
@@ -705,10 +891,11 @@ public class AnnotationPanel
{
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])
@@ -721,13 +908,13 @@ public class AnnotationPanel
if (row.hasText)
{
- iconOffset =av.charHeight -fm.getDescent();
+ iconOffset = av.charHeight - fm.getDescent();
y -= av.charHeight;
}
}
else if (row.hasText)
{
- iconOffset = av.charHeight -fm.getDescent();
+ iconOffset = av.charHeight - fm.getDescent();
}
else
@@ -735,29 +922,27 @@ public class AnnotationPanel
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.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"))
+ 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.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);
+ // g.drawString("Calculating Conservation.....",20, y-row.height/2);
continue;
}
@@ -765,23 +950,23 @@ public class AnnotationPanel
{
y += av.charHeight;
- g.drawImage(fadedImage,
- 0, y - row.height, imgWidth, y,
- 0, y - row.height, imgWidth, y, this);
+ 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);
+ // / g.drawString("Calculating Quality....",20, y-row.height/2);
continue;
}
-
-
- x = 0;
+ // first pass sets up state for drawing continuation from left-hand column
+ // of startRes
+ x = (startRes == 0) ? 0 : -1;
while (x < endRes - startRes)
{
if (av.hasHiddenColumns)
{
- column = av.getColumnSelection().adjustForHiddenColumns(startRes + x);
+ column = av.getColumnSelection().adjustForHiddenColumns(
+ startRes + x);
if (column > row.annotations.length - 1)
{
break;
@@ -792,8 +977,7 @@ public class AnnotationPanel
column = startRes + x;
}
- if ( (row.annotations==null)
- || (row.annotations.length <= column)
+ if ((row.annotations == null) || (row.annotations.length <= column)
|| (row.annotations[column] == null))
{
validRes = false;
@@ -802,222 +986,178 @@ public class AnnotationPanel
{
validRes = true;
}
-
- if (activeRow == i)
+ if (x > -1)
{
- g.setColor(Color.red);
-
- if (av.getColumnSelection() != null)
+ if (activeRow == i)
{
- for (int n = 0; n < av.getColumnSelection().size(); n++)
- {
- int v = av.getColumnSelection().columnAt(n);
+ g.setColor(Color.red);
- if (v == column)
+ if (av.getColumnSelection() != null)
+ {
+ for (int n = 0; n < av.getColumnSelection().size(); n++)
{
- g.fillRect(x * av.charWidth, y,
- av.charWidth, av.charHeight);
+ 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 (av.validCharWidth
+ && validRes
+ && row.annotations[column].displayCharacter != null
+ && (row.annotations[column].displayCharacter.length() > 0))
+ {
- int charOffset = (av.charWidth -
- fm.charWidth(row.annotations[column].
- displayCharacter.charAt(
- 0))) / 2;
+ if (centreColLabels || scaleColLabel)
+ {
+ fmWidth = (float) fm.charsWidth(
+ row.annotations[column].displayCharacter
+ .toCharArray(), 0,
+ row.annotations[column].displayCharacter.length());
- if (row.annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(row.annotations[column].colour);
+ 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 (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.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))
+ char ss = validRes ? row.annotations[column].secondaryStructure
+ : ' ';
+ if (ss == 'S')
{
- switch (lastSS)
+ // distinguish between forward/backward base-pairing
+ if (row.annotations[column].displayCharacter.indexOf(')') > -1)
{
+ ss = 's';
+ }
+ }
+ if (!validRes || (ss != lastSS))
+ {
+ if (x > -1)
+ {
+ 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);
+ drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
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);
+ drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ break;
+ case 'S': // Stem case for RNA secondary structure
+ case 's': // and opposite direction
+ drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
break;
default:
g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * av.charWidth) - lastSSX, 2);
+ g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+ - lastSSX, 2);
break;
+ }
}
-
if (validRes)
{
- lastSS = row.annotations[column].secondaryStructure;
+ lastSS = ss;
}
else
{
lastSS = ' ';
}
-
- lastSSX = (x * av.charWidth);
+ if (x > -1)
+ {
+ lastSSX = (x * av.charWidth);
+ }
}
}
-
column++;
x++;
}
-
if (column >= row.annotations.length)
{
column = row.annotations.length - 1;
+ validEnd = false;
+ }
+ else
+ {
+ validEnd = true;
}
- // x ++;
+ // 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 + 1) * av.charWidth - lastSSX, 7);
- }
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset,
- (x * av.charWidth) - lastSSX, 2);
-
- break;
+ case 'H':
+ drawHelixAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ break;
+
+ case 'E':
+ drawSheetAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ break;
+ case 's':
+ case 'S': // Stem case for RNA secondary structure
+ drawStemAnnot(g, row, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ break;
+ default:
+ drawGlyphLine(g, row, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ break;
}
}
@@ -1054,9 +1194,8 @@ public class AnnotationPanel
{
if (aa[gg].graphGroup == row.graphGroup)
{
- drawLineGraph(g, aa[gg], startRes, endRes, y,
- groupmin, groupmax,
- row.graphHeight);
+ drawLineGraph(g, aa[gg], startRes, endRes, y, groupmin,
+ groupmax, row.graphHeight);
}
}
@@ -1064,14 +1203,14 @@ public class AnnotationPanel
}
else
{
- drawLineGraph(g, row, startRes, endRes,
- y, row.graphMin, row.graphMax, row.graphHeight);
+ 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);
+ drawBarGraph(g, row, startRes, endRes, row.graphMin,
+ row.graphMax, y);
}
}
@@ -1087,11 +1226,159 @@ public class AnnotationPanel
}
}
- public void drawLineGraph(Graphics g, AlignmentAnnotation aa,
- int sRes, int eRes,
- int y,
- float min, float max,
- int graphHeight)
+ private void drawStemAnnot(Graphics g, AlignmentAnnotation row,
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
+ {
+ g.setColor(STEM_COLOUR);
+ int sCol = (lastSSX / av.charWidth) + startRes;
+ int x1 = lastSSX;
+ int x2 = (x * av.charWidth);
+ Regex closeparen = new Regex("(\\))");
+
+ String dc = column == 0 ? ""
+ : row.annotations[column - 1].displayCharacter;
+
+ boolean diffupstream = sCol == 0 || row.annotations[sCol - 1] == null
+ || !dc.equals(row.annotations[sCol - 1].displayCharacter);
+ boolean diffdownstream = !validRes || !validEnd
+ || row.annotations[column] == null
+ || !dc.equals(row.annotations[column].displayCharacter);
+ // System.out.println("Column "+column+" diff up: "+diffupstream+" down:"+diffdownstream);
+ // If a closing base pair half of the stem, display a backward arrow
+ if (column > 0 && closeparen.search(dc))
+ {
+ if (diffupstream)
+ // if (validRes && column>1 && row.annotations[column-2]!=null &&
+ // dc.equals(row.annotations[column-2].displayCharacter))
+ {
+ g.fillPolygon(new int[]
+ { lastSSX + 5, lastSSX + 5, lastSSX }, new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ x1 += 5;
+ }
+ if (diffdownstream)
+ {
+ x2 -= 1;
+ }
+ }
+ else
+ {
+ // display a forward arrow
+ if (diffdownstream)
+ {
+ g.fillPolygon(new int[]
+ { x2 - 5, x2 - 5, x2 }, new int[]
+ { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset }, 3);
+ x2 -= 5;
+ }
+ if (diffupstream)
+ {
+ x1 += 1;
+ }
+ }
+ // draw arrow body
+ g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 7);
+ }
+
+ private void drawGlyphLine(Graphics g, AlignmentAnnotation row,
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
+ {
+ g.setColor(Color.gray);
+ g
+ .fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
+ - lastSSX, 2);
+ }
+
+ private void drawSheetAnnot(Graphics g, AlignmentAnnotation row,
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
+ {
+ g.setColor(SHEET_COLOUR);
+
+ if (!validEnd || !validRes || row.annotations[column] == null
+ || row.annotations[column].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);
+ }
+
+ }
+
+ private void drawHelixAnnot(Graphics g, AlignmentAnnotation row,
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
+ {
+ g.setColor(HELIX_COLOUR);
+
+ int sCol = (lastSSX / av.charWidth) + startRes;
+ int x1 = lastSSX;
+ int x2 = (x * av.charWidth);
+
+ if (MAC)
+ {
+ int ofs = av.charWidth / 2;
+ // Off by 1 offset when drawing rects and ovals
+ // to offscreen image on the MAC
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1, 8, 8, 8);
+ if (sCol == 0 || row.annotations[sCol - 1] == null
+ || row.annotations[sCol - 1].secondaryStructure != 'H')
+ {
+ }
+ else
+ {
+ // g.setColor(Color.orange);
+ g.fillRoundRect(lastSSX, y + 4 + iconOffset, x2 - x1 - ofs + 1, 8,
+ 0, 0);
+ }
+ if (!validRes || row.annotations[column] == null
+ || row.annotations[column].secondaryStructure != 'H')
+ {
+
+ }
+ else
+ {
+ // g.setColor(Color.magenta);
+ g.fillRoundRect(lastSSX + ofs, y + 4 + iconOffset, x2 - x1 - ofs
+ + 1, 8, 0, 0);
+
+ }
+
+ return;
+ }
+
+ 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);
+ }
+
+ public void drawLineGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+ int eRes, int y, float min, float max, int graphHeight)
{
if (sRes > aa.annotations.length)
{
@@ -1100,7 +1387,7 @@ public class AnnotationPanel
int x = 0;
- //Adjustment for fastpaint to left
+ // Adjustment for fastpaint to left
if (eRes < av.endRes)
{
eRes++;
@@ -1116,10 +1403,10 @@ public class AnnotationPanel
int y1 = y, y2 = y;
float range = max - min;
- ////Draw origin
+ // //Draw origin
if (min < 0)
{
- y2 = y - (int) ( (0 - min / range) * graphHeight);
+ y2 = y - (int) ((0 - min / range) * graphHeight);
}
g.setColor(Color.gray);
@@ -1143,7 +1430,8 @@ public class AnnotationPanel
break;
}
- if (aa.annotations[column] == null || aa.annotations[column - 1] == null)
+ if (aa.annotations[column] == null
+ || aa.annotations[column - 1] == null)
{
x++;
continue;
@@ -1154,13 +1442,13 @@ public class AnnotationPanel
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);
+ 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);
+ g.drawLine(x * av.charWidth - av.charWidth / 2, y1, x * av.charWidth
+ + av.charWidth / 2, y2);
x++;
}
@@ -1168,28 +1456,29 @@ public class AnnotationPanel
{
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));
+ 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);
+ 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)
+ public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
+ int eRes, float min, float max, int y)
{
+ 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;
@@ -1198,7 +1487,7 @@ public class AnnotationPanel
if (min < 0)
{
- y2 = y - (int) ( (0 - min / (range)) * aa.graphHeight);
+ y2 = y - (int) ((0 - min / (range)) * aa.graphHeight);
}
g.setColor(Color.gray);
@@ -1207,7 +1496,21 @@ public class AnnotationPanel
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;
@@ -1226,46 +1529,165 @@ public class AnnotationPanel
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);
+ y1 = y
+ - (int) (((aa.annotations[column].value - min) / (range)) * aa.graphHeight);
- if (y1 - y2 > 0)
+ if (renderHistogram)
{
- g.fillRect(x * av.charWidth, y2, av.charWidth, y1 - y2);
+ 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);
+ }
}
- else
+ // draw profile if available
+ if (renderProfile && aa.annotations[column].value != 0)
{
- g.fillRect(x * av.charWidth, y1, av.charWidth, y2 - y1);
- }
- x++;
+ int profl[] = getProfileFor(aa, column);
+ // just try to draw the logo if profl is not null
+ if (profl != null)
+ {
+
+ int ht = y1, htn = y2 - y1;// aa.graphHeight;
+ float wdth;
+ double ht2 = 0;
+ char[] dc;
+
+ /**
+ * profl.length == 51 indicates that the profile of a secondary
+ * structure conservation row was accesed.
+ * Therefore dc gets length 2, to have space for a basepair instead of
+ * just a single nucleotide
+ */
+ if (profl.length == 51)
+ {
+ dc = new char[2];
+ }
+ else
+ {
+ dc = new char[1];
+ }
+
+ LineMetrics lm;
+ for (int c = 1; profl != null && c < profl[0];)
+ {
+ dc[0] = (char) profl[c++];
+ if (aa.label.startsWith("StrucConsensus"))
+ {
+ dc[1] = (char) profl[c++];
+ }
+
+ wdth = av.charWidth;
+ wdth /= (float) fm.charsWidth(dc, 0, dc.length);
+
+ 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));
+ // System.out.println(dc[0]);
+
+ g.drawChars(dc, 0, dc.length, 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));
+ 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);
+ y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
g2.setStroke(new BasicStroke());
}
}
+ private int[] getProfileFor(AlignmentAnnotation aa, int column)
+ {
+ 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());
+ }
+ }
+ else
+ {
+ if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
+ {
+ if (aa.groupRef != null && aa.groupRef.consensusData != null
+ && aa.groupRef.isShowSequenceLogo())
+ {
+ //TODO check what happens for group selections
+ return StructureFrequency.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 StructureFrequency.extractProfile(av.hStrucConsensus[column],
+ av.getIgnoreGapsConsensus());
+ }
+ }
+ }
+ return null;
+ }
+
// used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y,
- int sRes, int eRes)
+ 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);
@@ -1283,7 +1705,7 @@ public class AnnotationPanel
else
g.setColor(aa.annotations[j].colour);
- height = (int) ( (aa.annotations[j].value / aa.graphMax) * y);
+ height = (int) ((aa.annotations[j].value / aa.graphMax) * y);
if (height > y)
{
height = y;