X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationPanel.java;h=4974abe298ece727584841a26bbda892b3cd8334;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=c5da18b20cee674f9f35998ea3e5c0e4754aff13;hpb=0b1ca393b3e936f798048c8c92d52a31b3498fb0;p=jalview.git
diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index c5da18b..4974abe 100755
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -1,32 +1,52 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import jalview.datamodel.*;
-import jalview.schemes.ColourSchemeI;
-
-public class AnnotationPanel extends Panel implements AdjustmentListener,
- ActionListener, MouseListener, MouseMotionListener
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.renderer.AnnotationRenderer;
+import jalview.renderer.AwtRenderPanelI;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
+public class AnnotationPanel extends Panel implements AwtRenderPanelI,
+ AdjustmentListener, ActionListener, MouseListener,
+ MouseMotionListener
{
AlignViewport av;
@@ -34,21 +54,24 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
int activeRow = -1;
- Vector activeRes;
+ final String HELIX = "Helix";
- static String HELIX = "Helix";
+ final String SHEET = "Sheet";
- static String SHEET = "Sheet";
+ /**
+ * For RNA secondary structure "stems" aka helices
+ */
+ final String STEM = "RNA Helix";
- static String LABEL = "Label";
+ final String LABEL = "Label";
- static String REMOVE = "Remove Annotation";
+ final String REMOVE = "Remove Annotation";
- static String COLOUR = "Colour";
+ final String COLOUR = "Colour";
- static Color HELIX_COLOUR = Color.red.darker();
+ final Color HELIX_COLOUR = Color.red.darker();
- static Color SHEET_COLOUR = Color.green.darker().darker();
+ final Color SHEET_COLOUR = Color.green.darker().darker();
Image image;
@@ -59,51 +82,62 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
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;
-
- boolean mouseDragging=false;
-
+
+ boolean mouseDragging = false;
+
public static int GRAPH_HEIGHT = 40;
boolean MAC = false;
+ public final AnnotationRenderer renderer;
+
public AnnotationPanel(AlignmentPanel ap)
{
MAC = new jalview.util.Platform().isAMac();
this.ap = ap;
av = ap.av;
setLayout(null);
- adjustPanelHeight();
+ int height = adjustPanelHeight();
+ ap.apvscroll.setValues(0, getSize().height, 0, height);
addMouseMotionListener(this);
addMouseListener(this);
// ap.annotationScroller.getVAdjustable().addAdjustmentListener( this );
+ renderer = new AnnotationRenderer();
}
public AnnotationPanel(AlignViewport av)
{
this.av = av;
+ renderer = new AnnotationRenderer();
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- ap.alabels.setScrollOffset(-evt.getValue());
}
/**
* DOCUMENT ME!
*
* @param evt
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ if (aa == null)
+ {
+ return;
+ }
Annotation[] anot = aa[activeRow].annotations;
if (anot.length < av.getColumnSelection().getMax())
@@ -115,9 +149,12 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
}
String label = "";
- if (av.colSel != null && av.colSel.size() > 0
- && anot[av.colSel.getMin()] != null)
+ if (av.getColumnSelection() != null
+ && av.getColumnSelection().size() > 0
+ && anot[av.getColumnSelection().getMin()] != null)
+ {
label = anot[av.getColumnSelection().getMin()].displayCharacter;
+ }
if (evt.getActionCommand().equals(REMOVE))
{
@@ -144,8 +181,10 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
{
int index = av.getColumnSelection().columnAt(i);
- if (!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
@@ -166,8 +205,10 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
{
int index = av.getColumnSelection().columnAt(i);
- if (!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
@@ -193,6 +234,13 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
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;
@@ -208,25 +256,35 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
+ if (evt.getActionCommand().equals(STEM))
+ {
+ aa[activeRow].showAllColLabels = true;
+ }
}
for (int i = 0; i < av.getColumnSelection().size(); i++)
{
int index = av.getColumnSelection().columnAt(i);
- if (!av.colSel.isVisible(index))
+ if (!av.getColumnSelection().isVisible(index))
+ {
continue;
+ }
if (anot[index] == null)
{
anot[index] = new Annotation(label, "", type, 0);
}
- anot[index].secondaryStructure = type;
+ anot[index].secondaryStructure = type != 'S' ? type : label
+ .length() == 0 ? ' ' : label.charAt(0);
anot[index].displayCharacter = label;
}
}
+ av.getAlignment().validateAnnotation(aa[activeRow]);
+
+ ap.alignmentChanged();
adjustPanelHeight();
repaint();
@@ -239,20 +297,25 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
ap.alignFrame, "Enter Label", 400, 200, true);
if (dialog.accept)
+ {
return dialog.getName();
+ }
else
+ {
return null;
+ }
}
+ @Override
public void mousePressed(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
}
- int height = 0;
+ int height = -scrollOffset;
activeRow = -1;
for (int i = 0; i < aa.length; i++)
@@ -268,13 +331,12 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
{
activeRow = i;
}
- else if (aa[i].graph > 0)
+ else if (aa[i].graph > 0)
{
// Stretch Graph
graphStretch = i;
graphStretchY = evt.getY();
}
-
break;
}
@@ -288,13 +350,27 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
return;
}
- PopupMenu pop = new PopupMenu("Structure type");
- MenuItem item = new MenuItem(HELIX);
- item.addActionListener(this);
- pop.add(item);
- item = new MenuItem(SHEET);
- item.addActionListener(this);
- pop.add(item);
+ PopupMenu pop = new PopupMenu(
+ MessageManager.getString("label.structure_type"));
+ MenuItem item;
+ /*
+ * Just display the needed structure options
+ */
+ if (av.getAlignment().isNucleotide() == true)
+ {
+ item = new MenuItem(STEM);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ else
+ {
+ item = new MenuItem(HELIX);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new MenuItem(SHEET);
+ item.addActionListener(this);
+ pop.add(item);
+ }
item = new MenuItem(LABEL);
item.addActionListener(this);
pop.add(item);
@@ -310,38 +386,44 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
return;
}
- if (aa == null)
- {
- return;
- }
-
ap.scalePanel.mousePressed(evt);
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
graphStretch = -1;
graphStretchY = -1;
mouseDragging = false;
+ if (needValidating)
+ {
+ ap.validate();
+ needValidating = false;
+ }
ap.scalePanel.mouseReleased(evt);
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ boolean needValidating = false;
+
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (graphStretch > -1)
{
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight += graphStretchY
- evt.getY();
- if (av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight < 0)
+ if (av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight < 0)
{
- av.alignment.getAlignmentAnnotation()[graphStretch].graphHeight = 0;
+ av.getAlignment().getAlignmentAnnotation()[graphStretch].graphHeight = 0;
}
graphStretchY = evt.getY();
- adjustPanelHeight();
+ av.calcPanelHeight();
+ needValidating = true;
ap.paintAlignment(true);
}
else
@@ -350,16 +432,17 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
}
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
}
int row = -1;
- int height = 0;
+ int height = -scrollOffset;
for (int i = 0; i < aa.length; i++)
{
@@ -377,7 +460,7 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
int res = evt.getX() / av.getCharWidth() + av.getStartRes();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
res = av.getColumnSelection().adjustForHiddenColumns(res);
}
@@ -394,11 +477,13 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
}
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
ap.scalePanel.mouseEntered(evt);
}
+ @Override
public void mouseExited(MouseEvent evt)
{
ap.scalePanel.mouseExited(evt);
@@ -406,62 +491,32 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
public int adjustPanelHeight()
{
- // setHeight of panels
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- int height = 0;
-
- if (aa != null)
- {
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- continue;
- }
-
- aa[i].height = 0;
-
- if (aa[i].hasText)
- {
- aa[i].height += av.charHeight;
- }
-
- if (aa[i].hasIcons)
- {
- aa[i].height += 16;
- }
-
- if (aa[i].graph > 0)
- {
- aa[i].height += aa[i].graphHeight;
- }
-
- if (aa[i].height == 0)
- {
- aa[i].height = 20;
- }
+ return adjustPanelHeight(true);
+ }
- height += aa[i].height;
- }
- }
- else
+ public int adjustPanelHeight(boolean repaint)
+ {
+ int height = av.calcPanelHeight();
+ this.setSize(new Dimension(getSize().width, height));
+ if (repaint)
{
- height = 20;
+ repaint();
}
-
- this.setSize(getSize().width, height);
-
- repaint();
-
return height;
-
}
+ /**
+ * calculate the height for visible annotation, revalidating bounds where
+ * necessary ABSTRACT GUI METHOD
+ *
+ * @return total height of annotation
+ */
+
public void addEditableColumn(int i)
{
if (activeRow == -1)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (aa == null)
{
return;
@@ -476,31 +531,28 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
}
}
}
-
- if (activeRes == null)
- {
- activeRes = new Vector();
- activeRes.addElement(String.valueOf(i));
- return;
- }
-
- activeRes.addElement(String.valueOf(i));
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
-
- imgWidth = getSize().width;
+ Dimension d = getSize();
+ imgWidth = d.width;
// (av.endRes - av.startRes + 1) * av.charWidth;
-
- if (image == null || imgWidth != image.getWidth(this))
+ if (imgWidth < 1 || d.height < 1)
{
- image = createImage(imgWidth, ap.annotationPanel.getSize().height);
+ return;
+ }
+ if (image == null || imgWidth != image.getWidth(this)
+ || d.height != image.getHeight(this))
+ {
+ image = createImage(imgWidth, d.height);
gg = image.getGraphics();
gg.setFont(av.getFont());
fm = gg.getFontMetrics();
@@ -523,20 +575,21 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
public void fastPaint(int horizontal)
{
- if (horizontal == 0 || av.alignment.getAlignmentAnnotation() == null
- || av.alignment.getAlignmentAnnotation().length < 1)
+ if (horizontal == 0
+ || av.getAlignment().getAlignmentAnnotation() == null
+ || av.getAlignment().getAlignmentAnnotation().length < 1)
{
repaint();
return;
}
- gg.copyArea(0, 0, imgWidth, getSize().height, -horizontal
- * av.charWidth, 0);
+ gg.copyArea(0, 0, imgWidth, getSize().height,
+ -horizontal * av.getCharWidth(), 0);
int sr = av.startRes, er = av.endRes + 1, transX = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * av.getCharWidth();
sr = er - horizontal;
}
else if (horizontal < 0)
@@ -558,11 +611,11 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
* DOCUMENT ME!
*
* @param g
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param startRes
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param endRes
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void drawComponent(Graphics g, int startRes, int endRes)
{
@@ -570,665 +623,78 @@ public class AnnotationPanel extends Panel implements AdjustmentListener,
g.setFont(ofont);
g.setColor(Color.white);
- g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getSize().height);
+ g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(),
+ getSize().height);
if (fm == null)
{
fm = g.getFontMetrics();
}
- if ((av.alignment.getAlignmentAnnotation() == null)
- || (av.alignment.getAlignmentAnnotation().length < 1))
+ if ((av.getAlignment().getAlignmentAnnotation() == null)
+ || (av.getAlignment().getAlignmentAnnotation().length < 1))
{
g.setColor(Color.white);
g.fillRect(0, 0, getSize().width, getSize().height);
g.setColor(Color.black);
if (av.validCharWidth)
{
- g.drawString("Alignment has no annotations", 20, 15);
+ g.drawString(MessageManager
+ .getString("label.alignment_has_no_annotations"), 20, 15);
}
return;
}
-
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
-
- int x = 0;
- int y = 0;
- int column = 0;
- char lastSS;
- int lastSSX;
- int iconOffset = av.charHeight / 2;
- boolean validRes = false;
- boolean 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.
- // \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;
- }
- }
- //TODO: else is the logic used in application, applet had no 'else'
- else if (row.hasText)
- {
- iconOffset = av.charHeight - fm.getDescent();
-
- }
- else
- {
- iconOffset = 0;
- }
-
- x = 0;
- while (x < endRes - startRes)
- {
- if (av.hasHiddenColumns)
- {
- column = av.getColumnSelection().adjustForHiddenColumns(
- startRes + x);
- if (column > row.annotations.length - 1)
- {
- break;
- }
- }
- else
- {
- column = startRes + x;
- }
-
- if ((row.annotations.length <= column)
- || (row.annotations[column] == null))
- {
- validRes = false;
- }
- else
- {
- validRes = true;
- }
-
- if (activeRow == i)
- {
- g.setColor(Color.red);
-
- if (av.getColumnSelection() != null)
- {
- for (int n = 0; n < av.getColumnSelection().size(); n++)
- {
- int v = av.getColumnSelection().columnAt(n);
-
- if (v == column)
- {
- g
- .fillRect(x * av.charWidth, y, av.charWidth,
- av.charHeight);
- }
- }
- }
- }
-
- if (av.validCharWidth
- && validRes
- && (row.annotations[column].displayCharacter != 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;
- // not 1.1 // g.setFont(new Font(ofont,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 + 3); // + 3?
- }
- 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 + 3); // +3?
- }
- g.setFont(ofont);
- }
-
- if (row.hasIcons)
- {
- if (!validRes
- || (row.annotations[column].secondaryStructure != lastSS))
- {
- switch (lastSS)
- {
- case 'H':
- g.setColor(HELIX_COLOUR);
- if (MAC)
- {
- // Off by 1 offset when drawing rects and ovals
- // to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset,
- (x * av.charWidth) - lastSSX, 7, 8, 8);
- break;
- }
-
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
-
- if (sCol == 0
- || row.annotations[sCol - 1] == null
- || row.annotations[sCol - 1].secondaryStructure != 'H')
- {
- g.fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8, 90,
- 180);
- x1 += av.charWidth / 2;
- }
-
- if (!validRes || row.annotations[column] == null
- || row.annotations[column].secondaryStructure != 'H')
- {
- g.fillArc((x * av.charWidth) - av.charWidth, y + 4
- + iconOffset, av.charWidth, 8, 270, 180);
- x2 -= av.charWidth / 2;
- }
-
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
- break;
-
- case 'E':
- g.setColor(SHEET_COLOUR);
- g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
- - lastSSX - 4, 7);
- g.fillPolygon(new int[]
- { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
- (x * av.charWidth) }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 8 + iconOffset },
- 3);
-
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
- - lastSSX, 2);
-
- break;
- }
-
- if (validRes)
- {
- lastSS = row.annotations[column].secondaryStructure;
- }
- else
- {
- lastSS = ' ';
- }
-
- lastSSX = (x * av.charWidth);
- }
- }
-
- column++;
- x++;
- }
-
- if (column >= row.annotations.length)
- {
- column = row.annotations.length - 1;
- validEnd = false;
- }
- else
- {
- validEnd = true;
- }
-
- // x ++;
-
- if (row.hasIcons)
- {
- switch (lastSS)
- {
- case 'H':
- g.setColor(HELIX_COLOUR);
- if (MAC)
- {
- // Off by 1 offset when drawing rects and ovals
- // to offscreen image on the MAC
- g.fillRoundRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
- - lastSSX, 7, 8, 8);
- break;
- }
-
- int sCol = (lastSSX / av.charWidth) + startRes;
- int x1 = lastSSX;
- int x2 = (x * av.charWidth);
-
- if (sCol == 0 || row.annotations[sCol - 1] == null
- || row.annotations[sCol - 1].secondaryStructure != 'H')
- {
- g
- .fillArc(lastSSX, y + 4 + iconOffset, av.charWidth, 8,
- 90, 180);
- x1 += av.charWidth / 2;
- }
-
- if (row.annotations[column] == null
- || row.annotations[column].secondaryStructure != 'H')
- {
- g.fillArc((x * av.charWidth) - av.charWidth,
- y + 4 + iconOffset, av.charWidth, 8, 270, 180);
- x2 -= av.charWidth / 2;
- }
-
- g.fillRect(x1, y + 4 + iconOffset, x2 - x1, 8);
-
- break;
-
- case 'E':
- g.setColor(SHEET_COLOUR);
-
- if (!validEnd || row.annotations[endRes] == null
- || row.annotations[endRes].secondaryStructure != 'E')
- {
- g.fillRect(lastSSX, y + 4 + iconOffset, (x * av.charWidth)
- - lastSSX - 4, 7);
- g.fillPolygon(new int[]
- { (x * av.charWidth) - 4, (x * av.charWidth) - 4,
- (x * av.charWidth) }, new int[]
- { y + iconOffset, y + 14 + iconOffset, y + 7 + iconOffset }, 3);
- }
- else
- {
- g.fillRect(lastSSX, y + 4 + iconOffset, x * av.charWidth
- - lastSSX, 7);
- }
- break;
-
- default:
- g.setColor(Color.gray);
- if (!av.wrapAlignment || endRes == av.endRes)
- {
- g.fillRect(lastSSX, y + 6 + iconOffset, (x * av.charWidth)
- - lastSSX, 2);
- }
-
- break;
- }
- }
-
- if (row.graph > 0 && 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;
- }
- }
+ g.translate(0, -scrollOffset);
+ renderer.drawComponent(this, av, g, activeRow, startRes, endRes);
+ g.translate(0, +scrollOffset);
}
- 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);
-
- int y1 = y, y2 = y;
- float range = max - min;
-
- // //Draw origin
- if (min < 0)
- {
- y2 = y - (int) ((0 - min / range) * graphHeight);
- }
+ int scrollOffset = 0;
- g.setColor(Color.gray);
- g.drawLine(x - av.charWidth, y2, (eRes - sRes) * av.charWidth, y2);
-
- eRes = Math.min(eRes, aa.annotations.length);
-
- int column;
- int aaMax = aa.annotations.length - 1;
-
- while (x < eRes - sRes)
- {
- column = sRes + x;
- if (av.hasHiddenColumns)
- {
- column = av.getColumnSelection().adjustForHiddenColumns(column);
- }
-
- if (column > aaMax)
- {
- break;
- }
-
- if (aa.annotations[column] == null) // || coaa.annotations[column - 1] ==
- // null)
- {
- x++;
- continue;
- }
-
- if (aa.annotations[column].colour == null)
- g.setColor(Color.black);
- else
- g.setColor(aa.annotations[column].colour);
- if (column == 0 || aa.annotations[column - 1] == null)
- {
- y1 = y
- - (int) (((aa.annotations[column].value - min) / range) * graphHeight);
- }
- else
- {
- 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)
+ public void setScrollOffset(int value, boolean repaint)
+ {
+ scrollOffset = value;
+ if (repaint)
{
- g.setColor(aa.threshold.colour);
-
- y2 = (int) (y - ((aa.threshold.value - min) / range) * graphHeight);
- g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
+ repaint();
}
}
- public void drawBarGraph(Graphics g, AlignmentAnnotation aa, int sRes,
- int eRes, float min, float max, int y)
+ @Override
+ public FontMetrics getFontMetrics()
{
- 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 = false;
- /* Logos are disabled for 2.5 release : Bug # 0060064
- * 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
- // Disabled for 2.5 release: see bug #0060064
- /**
- if (aa.annotations[column].value!=0 && renderProfile)
- {
- int profl[] = getProfileFor(aa,column);
- int ht = y1; //,htn=y2-y1;//aa.graphHeight;
- float wdth;
- double ht2=0;
- char[] dc = new char[1];
- // LineMetrics lm;
- for (int c=1;profl!=null && c2)
- {
- ht+=(int)ht2;
- }
- {
- // not java 1.1 compatible: Bug # 0060064
- g.setFont(ofont.deriveFont(AffineTransform.getScaleInstance(wdth, (ht2=(htn*((double)profl[c++])/100.0))/av.charHeight)));
- lm = g.getFontMetrics().getLineMetrics(dc,0,1, g);
- g.setColor(profcolour.findColour(dc[0]));
- g.drawChars(dc,0,1,x*av.charWidth, (int) (ht+lm.getHeight()));
- }
- }
- g.setFont(ofont);
- }
- **/
- x++;
-
- }
- if (aa.threshold != null)
- {
- g.setColor(aa.threshold.colour);
- y2 = (int) (y - ((aa.threshold.value - min) / range) * aa.graphHeight);
- g.drawLine(0, y2, (eRes - sRes) * av.charWidth, y2);
- }
+ return fm;
}
- /*
- * Disabled for 2.5 release - see bug #0060064
- private int[] getProfileFor(AlignmentAnnotation aa, int column)
+ @Override
+ public Image getFadedImage()
{
-// if (aa.autoCalculated && aa.label.startsWith("Consensus")) {
- if (aa.groupRef!=null && aa.groupRef.consensusData!=null) { // && aa.groupRef.isShowSequenceLogo()) {
- return AAFrequency.extractProfile(aa.groupRef.consensusData[column],aa.groupRef.getIgnoreGapsConsensus());
- }
- // TODO extend annotation row to enable dynamic and static profile data to be stored
- if (aa.groupRef==null && aa.sequenceRef==null) // && av.isShowSequenceLogo())
- {
- return AAFrequency.extractProfile(av.hconsensus[column],av.getIgnoreGapsConsensus());
- }
- // }
- return null;
+ return image;
}
- */
- // used by overview window
- public void drawGraph(Graphics g, AlignmentAnnotation aa, int width,
- int y, int sRes, int eRes)
+ @Override
+ public int getFadedImageWidth()
{
- eRes = Math.min(eRes, aa.annotations.length);
- g.setColor(Color.white);
- g.fillRect(0, 0, width, y);
- g.setColor(new Color(0, 0, 180));
+ return imgWidth;
+ }
- int x = 0, height;
+ private int[] bounds = new int[2];
- for (int j = sRes; j < eRes; j++)
+ @Override
+ public int[] getVisibleVRange()
+ {
+ if (ap != null && ap.alabels != 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) * GRAPH_HEIGHT);
- if (height > y)
- {
- height = y;
- }
- g.fillRect(x, y - height, av.charWidth, height);
- x += av.charWidth;
+ int sOffset = -ap.alabels.scrollOffset;
+ int visHeight = sOffset + ap.annotationPanelHolder.getHeight();
+ bounds[0] = sOffset;
+ bounds[1] = visHeight;
+ return bounds;
+ }
+ else
+ {
+ return null;
}
}
}