X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=a88aa4a4ee30b6e5ea5920c84140c92bd5af46dc;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=8a220b86d198f4938f3ca5720d6074620d986fe9;hpb=c80420d1cb6b2aac106501d16f4ecffbcd200c0a;p=jalview.git
diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 8a220b8..a88aa4a 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1,874 +1,1720 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.datamodel.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-
-import java.util.*;
-
-import javax.swing.*;
-
-
-/**
- * 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();
-
- /** DOCUMENT ME!! */
- public static int GRAPH_HEIGHT = 40;
- AlignViewport av;
- AlignmentPanel ap;
- int activeRow = -1;
- Vector activeRes;
- BufferedImage image;
- Graphics2D gg;
- FontMetrics fm;
- int imgWidth = 0;
- boolean fastPaint = false;
-
- /**
- * Creates a new AnnotationPanel object.
- *
- * @param ap DOCUMENT ME!
- */
- 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);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- ap.alabels.setScrollOffset(-evt.getValue());
- }
-
- /**
- * DOCUMENT ME!
- */
- public void adjustPanelHeight()
- {
- // setHeight of panels
- image = null;
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- int height = 0;
-
- if (aa != null)
- {
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- continue;
- }
-
- aa[i].height = 0;
-
- if (aa[i].hasText)
- {
- aa[i].height += av.charHeight;
- }
-
- if (aa[i].hasIcons)
- {
- aa[i].height += 16;
- }
-
- if (aa[i].isGraph)
- {
- aa[i].height += GRAPH_HEIGHT;
- }
-
- if (aa[i].height == 0)
- {
- aa[i].height = 20;
- }
-
- height += aa[i].height;
- }
- }
- else
- {
- height = 20;
- }
-
- this.setPreferredSize(new Dimension(1, height));
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param col DOCUMENT ME!
- */
- public void removeEditableColumn(int col)
- {
- if (activeRow == -1)
- {
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- if(aa==null)
- return;
-
- for (int j = 0; j < aa.length; j++)
- {
- if (aa[j].editable)
- {
- activeRow = j;
-
- break;
- }
- }
- }
-
- if ((activeRes != null) && activeRes.contains(String.valueOf(col)))
- {
- activeRes.removeElement(String.valueOf(col));
- }
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param col DOCUMENT ME!
- */
- public void addEditableColumn(int col)
- {
- if (activeRow == -1)
- {
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- if(aa==null)
- return;
-
- for (int j = 0; j < aa.length; j++)
- {
- if (aa[j].editable)
- {
- activeRow = j;
-
- break;
- }
- }
- }
-
- if (activeRes == null)
- {
- activeRes = new Vector();
- }
-
- if (!activeRes.contains(String.valueOf(col)))
- {
- activeRes.addElement(String.valueOf(col));
- }
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void actionPerformed(ActionEvent evt)
- {
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- Annotation[] anot = aa[activeRow].annotations;
-
- 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 (label == null)
- {
- return;
- }
-
- if ((label.length() > 0) && !aa[activeRow].hasText)
- {
- aa[activeRow].hasText = true;
- }
-
- for (int i = 0; i < activeRes.size(); i++)
- {
- int index = Integer.parseInt(activeRes.get(i).toString());
-
- if (anot[index] == null)
- {
- anot[index] = new Annotation(label, "", ' ', 0);
- }
-
- anot[index].displayCharacter = label;
- }
- }
- else if (evt.getActionCommand().equals(COLOUR))
- {
- Color col = JColorChooser.showDialog(this,
- "Choose foreground colour", Color.black);
-
- 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);
- }
-
- anot[index].colour = col;
- }
- }
- else // HELIX OR SHEET
- {
- char type = 0;
- String symbol = "\u03B1";
-
- if (evt.getActionCommand().equals(HELIX))
- {
- type = 'H';
- }
- else if (evt.getActionCommand().equals(SHEET))
- {
- type = 'E';
- symbol = "\u03B2";
- }
-
- if (!aa[activeRow].hasIcons)
- {
- aa[activeRow].hasIcons = true;
- }
-
- 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 < activeRes.size(); i++)
- {
- int index = Integer.parseInt(activeRes.get(i).toString());
-
- if (anot[index] == null)
- {
- anot[index] = new Annotation(label, "", type, 0);
- }
-
- anot[index].secondaryStructure = type;
- anot[index].displayCharacter = label;
- }
- }
-
- adjustPanelHeight();
- activeRes = null;
- repaint();
-
- return;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mousePressed(MouseEvent evt)
- {
- int height = 0;
- activeRow = -1;
-
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
- for (int i = 0; i < aa.length; i++)
- {
- if (aa[i].visible)
- {
- height += aa[i].height;
- }
-
- if (evt.getY() < height)
- {
- if (aa[i].editable)
- {
- activeRow = i;
- }
- else
- {
- activeRes = null;
- }
-
- break;
- }
- }
-
- if (SwingUtilities.isRightMouseButton(evt))
- {
- if (activeRes == null)
- {
- 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;
- }
-
- if (aa == null)
- {
- return;
- }
-
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
- if (evt.isControlDown() || evt.isAltDown())
- {
- addEditableColumn(res);
- }
- else if (evt.isShiftDown())
- {
- if (activeRes == null)
- {
- activeRes = new Vector();
- }
- else
- {
- int start = Integer.parseInt(activeRes.get(activeRes.size() -
- 1).toString());
- int end = res;
-
- if (end < start)
- {
- int temp = end;
- end = start;
- start = temp;
- }
-
- for (int n = start; n <= end; n++)
- {
- addEditableColumn(n);
- }
- }
- }
- else
- {
- activeRes = new Vector();
- activeRes.addElement(String.valueOf(res));
- }
-
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseExited(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseMoved(MouseEvent evt)
- {
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
- if (aa == null)
- {
- return;
- }
-
- int row = -1;
- int height = 0;
-
- for (int i = 0; i < aa.length; i++)
- {
- if (aa[i].visible)
- {
- height += aa[i].height;
- }
-
- if (evt.getY() < height)
- {
- row = i;
-
- break;
- }
- }
-
- int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-
- if ((row > -1) && (res < aa[row].annotations.length) &&
- (aa[row].annotations[res] != null))
- {
- this.setToolTipText(aa[row].annotations[res].description);
-
- StringBuffer text = new StringBuffer("Sequence position " +
- (res + 1) + " " + aa[row].annotations[res].description);
- ap.alignFrame.statusBar.setText(text.toString());
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent evt)
- {
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void paintComponent(Graphics g)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
-
- if (fastPaint && image!=null)
- {
- g.drawImage(image, 0, 0, this);
- fastPaint = false;
- return;
- }
-
- imgWidth = (av.endRes - av.startRes + 1) * av.charWidth;
-
- if (image == null || imgWidth != image.getWidth())
- {
- image = new BufferedImage(imgWidth, ap.annotationPanel.getHeight(),
- BufferedImage.TYPE_INT_RGB);
- gg = (Graphics2D) image.getGraphics();
- gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
-
- gg.setFont(av.getFont());
- fm = gg.getFontMetrics();
- }
-
- drawComponent(gg, av.startRes, av.endRes + 1);
- g.drawImage(image, 0, 0, this);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param horizontal DOCUMENT ME!
- */
- public void fastPaint(int horizontal)
- {
- if ((horizontal == 0) ||
- (av.alignment.getAlignmentAnnotation() == null) ||
- (av.alignment.getAlignmentAnnotation().length < 1))
- {
- repaint();
-
- return;
- }
-
- gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
-
- int sr = av.startRes;
- int er = av.endRes + 1;
- int transX = 0;
-
- if (horizontal > 0) // scrollbar pulled right, image to the left
- {
- transX = (er - sr - horizontal) * av.charWidth;
- sr = er - horizontal;
- }
- else if (horizontal < 0)
- {
- er = sr - horizontal;
- }
-
- gg.translate(transX, 0);
-
- drawComponent(gg, sr, er);
-
- gg.translate(-transX, 0);
-
- fastPaint = true;
-
- repaint();
-
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- * @param startRes DOCUMENT ME!
- * @param endRes DOCUMENT ME!
- */
- public void drawComponent(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);
-
- return;
- }
-
- 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)
- {
- y -= av.charHeight;
- }
- }
-
- 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;
- }
-
- x = (j - startRes) * av.charWidth;
-
- if (activeRow == i)
- {
- g.setColor(Color.red);
-
- if (activeRes != null)
- {
- for (int n = 0; n < activeRes.size(); n++)
- {
- int v = Integer.parseInt(activeRes.get(n).toString());
-
- if (v == j)
- {
- g.fillRect((j - startRes) * av.charWidth, y,
- av.charWidth, row.height);
- }
- }
- }
- }
-
- 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 || row.isGraph)
- {
- g.drawString(row.annotations[j].displayCharacter, x+charOffset,
- y + iconOffset + 3);
- }
- else if (((row.annotations[j - 1] == null) ||
- (row.annotations[j].displayCharacter != row.annotations[j -
- 1].displayCharacter)))
- {
- g.drawString(row.annotations[j].displayCharacter, x+charOffset,
- y + iconOffset + 3);
- }
- }
-
- if (row.hasIcons)
- {
- if (!validRes ||
- (row.annotations[j].secondaryStructure != lastSS[i]))
- {
- switch (lastSS[i])
- {
- case 'H':
- g.setColor(HELIX_COLOUR);
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
- x - lastSSX[i], 7, 8, 8);
-
- 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 + 8 + iconOffset
- }, 3);
-
- break;
-
- case 'C':
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX[i], y + 6 + iconOffset,
- x - lastSSX[i], 2);
-
- break;
- }
-
- if (validRes)
- {
- lastSS[i] = row.annotations[j].secondaryStructure;
- }
- else
- {
- lastSS[i] = ' ';
- }
-
- lastSSX[i] = x;
- }
- }
-
- if (validRes && row.isGraph)
- {
- g.setColor(new Color(0, 0, 180));
-
- int height = (int) ((row.annotations[j].value / row.graphMax) * GRAPH_HEIGHT);
-
- if (row.windowLength > 1)
- {
- int total = 0;
-
- for (int i2 = j - (row.windowLength / 2);
- i2 < (j + (row.windowLength / 2)); i2++)
- {
- if ((i2 < 0) || (i2 >= av.alignment.getWidth()))
- {
- continue;
- }
-
- total += row.annotations[i2].value;
- }
-
- total /= row.windowLength;
- height = (int) ((total / row.graphMax) * GRAPH_HEIGHT);
- }
-
- g.setColor(row.annotations[j].colour);
- g.fillRect(x, y - height, av.charWidth, height);
- }
- }
-
- x += av.charWidth;
-
- if (row.hasIcons)
- {
- switch (lastSS[i])
- {
- case 'H':
- g.setColor(HELIX_COLOUR);
- g.fillRoundRect(lastSSX[i], y + 4 + iconOffset,
- x - lastSSX[i], 7, 8, 8);
-
- 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);
-
- break;
-
- case 'C':
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX[i], y + 6 + iconOffset, x - lastSSX[i], 2);
-
- break;
- }
- }
-
- if (row.isGraph && row.hasText)
- {
- y += av.charHeight;
- }
-
- if (!row.isGraph)
- {
- y += aa[i].height;
- }
- }
- }
-
- // used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width, int y, int sRes, int eRes)
- {
- g.setColor(Color.white);
- g.fillRect(0, 0, width, y);
- g.setColor(new Color(0, 0, 180));
-
-
- int x = 0, height;
-
- for (int j = sRes; j < eRes; j++)
- {
- g.setColor(new Color(0, 0, 180));
-
- height = (int) ((aa.annotations[j].value / aa.graphMax) * GRAPH_HEIGHT);
- if(height>y)
- height = y;
-
- g.fillRect(x, y - height, av.charWidth, height);
- x += av.charWidth;
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 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
+{
+ 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
+ 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;
+
+ // for editing cursor
+ int cursorX = 0;
+
+ int cursorY = 0;
+
+ /**
+ * Creates a new AnnotationPanel object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ */
+ public AnnotationPanel(AlignmentPanel ap)
+ {
+
+ MAC = new jalview.util.Platform().isAMac();
+
+ 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 AnnotationPanel(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void adjustmentValueChanged(AdjustmentEvent evt)
+ {
+ ap.alabels.setScrollOffset(-evt.getValue());
+ }
+
+ /**
+ * 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;
+
+ 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;
+ }
+ }
+ if (height == 0)
+ {
+ // set minimum
+ height = 20;
+ }
+ return height;
+ }
+
+ /**
+ * 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())
+ {
+ Annotation[] temp = new Annotation[av.getColumnSelection().getMax() + 2];
+ System.arraycopy(anot, 0, temp, 0, anot.length);
+ anot = temp;
+ aa[activeRow].annotations = anot;
+ }
+
+ if (evt.getActionCommand().equals(REMOVE))
+ {
+ for (int i = 0; i < av.getColumnSelection().size(); i++)
+ {
+ anot[av.getColumnSelection().columnAt(i)] = null;
+ }
+ }
+ else if (evt.getActionCommand().equals(LABEL))
+ {
+ 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)
+ {
+ aa[activeRow].hasText = true;
+ }
+
+ for (int i = 0; i < av.getColumnSelection().size(); i++)
+ {
+ int index = av.getColumnSelection().columnAt(i);
+
+ if (!av.colSel.isVisible(index))
+ continue;
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
+ // null exceptions
+ // aren't raised
+ // elsewhere.
+ }
+ else
+ {
+ anot[index].displayCharacter = label;
+ }
+ }
+ }
+ else if (evt.getActionCommand().equals(COLOUR))
+ {
+ Color col = JColorChooser.showDialog(this,
+ "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))
+ continue;
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation("", "", ' ', 0);
+ }
+
+ anot[index].colour = col;
+ }
+ }
+ else
+ // HELIX OR SHEET
+ {
+ char type = 0;
+ String symbol = "\u03B1";
+
+ if (evt.getActionCommand().equals(HELIX))
+ {
+ type = 'H';
+ }
+ else if (evt.getActionCommand().equals(SHEET))
+ {
+ type = 'E';
+ symbol = "\u03B2";
+ }
+
+ // Added by LML to color stems
+ else if (evt.getActionCommand().equals(STEM))
+ {
+ type = 'S';
+ symbol = "\u03C3";
+ }
+
+ if (!aa[activeRow].hasIcons)
+ {
+ aa[activeRow].hasIcons = true;
+ }
+
+ 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 (!av.colSel.isVisible(index))
+ continue;
+
+ if (anot[index] == null)
+ {
+ anot[index] = new Annotation(label, "", type, 0);
+ }
+
+ anot[index].secondaryStructure = type;
+ anot[index].displayCharacter = label;
+ }
+ }
+
+ adjustPanelHeight();
+ repaint();
+
+ return;
+ }
+
+ 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!
+ */
+ public void mousePressed(MouseEvent evt)
+ {
+
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
+
+ int height = 0;
+ activeRow = -1;
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].visible)
+ {
+ height += aa[i].height;
+ }
+
+ if (evt.getY() < height)
+ {
+ if (aa[i].editable)
+ {
+ activeRow = i;
+ }
+ else if (aa[i].graph > 0)
+ {
+ // Stretch Graph
+ graphStretch = i;
+ graphStretchY = evt.getY();
+ }
+
+ break;
+ }
+ }
+
+ if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1)
+ {
+ if (av.getColumnSelection() == null)
+ {
+ return;
+ }
+
+ JPopupMenu pop = new JPopupMenu("Structure type");
+ 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);
+ 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)
+ {
+ return;
+ }
+
+ ap.scalePanel.mousePressed(evt);
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent evt)
+ {
+ graphStretch = -1;
+ graphStretchY = -1;
+ mouseDragging = false;
+ ap.scalePanel.mouseReleased(evt);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent evt)
+ {
+ ap.scalePanel.mouseEntered(evt);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent evt)
+ {
+ ap.scalePanel.mouseExited(evt);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseDragged(MouseEvent evt)
+ {
+ if (graphStretch > -1)
+ {
+ 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.paintAlignment(true);
+ }
+ else
+ {
+ ap.scalePanel.mouseDragged(evt);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent evt)
+ {
+ AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+
+ if (aa == null)
+ {
+ this.setToolTipText(null);
+ return;
+ }
+
+ int row = -1;
+ int height = 0;
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i].visible)
+ {
+ height += aa[i].height;
+ }
+
+ if (evt.getY() < height)
+ {
+ row = i;
+
+ break;
+ }
+ }
+
+ if (row == -1)
+ {
+ this.setToolTipText(null);
+ return;
+ }
+
+ int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+
+ if (av.hasHiddenColumns)
+ {
+ res = av.getColumnSelection().adjustForHiddenColumns(res);
+ }
+
+ 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)
+ {
+ 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
+ && 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));
+
+ if (aa[row].annotations[res].description != null)
+ {
+ text.append(" " + aa[row].annotations[res].description);
+ }
+
+ ap.alignFrame.statusBar.setText(text.toString());
+ }
+ }
+ else
+ {
+ this.setToolTipText(null);
+ }
+ }
+
+ /**
+ * 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!
+ */
+ public void paintComponent(Graphics g)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+
+ 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;
+ if (imgWidth < 1)
+ return;
+ 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());
+ }
+
+ drawComponent(gg, av.startRes, av.endRes + 1);
+ g.drawImage(image, 0, 0, this);
+ }
+
+ /**
+ * 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)
+ {
+ repaint();
+ return;
+ }
+ gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0);
+
+ int sr = av.startRes;
+ int er = av.endRes + 1;
+ int transX = 0;
+
+ if (horizontal > 0) // scrollbar pulled right, image to the left
+ {
+ transX = (er - sr - horizontal) * av.charWidth;
+ sr = er - horizontal;
+ }
+ else if (horizontal < 0)
+ {
+ er = sr - horizontal;
+ }
+
+ gg.translate(transX, 0);
+
+ drawComponent(gg, sr, er);
+
+ gg.translate(-transX, 0);
+
+ fastPaint = true;
+ repaint();
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
+ * @param endRes
+ * DOCUMENT ME!
+ */
+ public void drawComponent(Graphics g, int startRes, int endRes)
+ {
+ if (av.updatingConsensus || av.updatingConservation)
+ {
+ if (image == null)
+ {
+ 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())
+ {
+ 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(
+ AlphaComposite.SRC_OVER, .3f));
+ fadedG.drawImage(image, 0, 0, this);
+
+ }
+
+ }
+ else
+ {
+ fadedImage = null;
+ }
+
+ g.setColor(Color.white);
+ g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight());
+
+ g.setFont(av.getFont());
+ if (fm == null)
+ {
+ fm = g.getFontMetrics();
+ }
+
+ if ((av.alignment.getAlignmentAnnotation() == null)
+ || (av.alignment.getAlignmentAnnotation().length < 1))
+ {
+ 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;
+ }
+
+ 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++)
+ {
+ 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;
+ }
+
+ // 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);
+ 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 (x > -1)
+ {
+ 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)
+ {
+ char ss = validRes ? row.annotations[column].secondaryStructure
+ : ' ';
+ if (ss == 'S')
+ {
+ // 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':
+ 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': // 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);
+
+ break;
+ }
+ }
+ if (validRes)
+ {
+ lastSS = ss;
+ }
+ else
+ {
+ lastSS = ' ';
+ }
+ 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 ++;
+
+ if (row.hasIcons)
+ {
+ switch (lastSS)
+ {
+ 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;
+ }
+ }
+
+ 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;
+ }
+ }
+ }
+
+ 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)
+ {
+ 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());
+ }
+ }
+
+ 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;
+
+ 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 (renderProfile && aa.annotations[column].value != 0)
+ {
+
+ 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));
+
+ 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)
+ {
+ eRes = Math.min(eRes, aa.annotations.length);
+ g.setColor(Color.white);
+ g.fillRect(0, 0, width, y);
+ g.setColor(new Color(0, 0, 180));
+
+ int x = 0, height;
+
+ for (int j = sRes; j < eRes; j++)
+ {
+ if (aa.annotations[j] != 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;
+ }
+ }
+
+}