X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=d5b2f492e7a7c1c241c7d90420d56f004a8bb616;hb=2273eba5668e5340354da60fed329c6c716cc439;hp=d951aba819ea80526609d64018fb32aee4bae552;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index d951aba..d5b2f49 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -1,19 +1,21 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
@@ -25,6 +27,7 @@ import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ResidueProperties;
import java.awt.BasicStroke;
import java.awt.Color;
@@ -52,13 +55,17 @@ public class AnnotationRenderer
{
this(false);
}
+
/**
* Create a new annotation Renderer
- * @param debugRedraw flag indicating if timing and redraw parameter info should be output
+ *
+ * @param debugRedraw
+ * flag indicating if timing and redraw parameter info should be
+ * output
*/
public AnnotationRenderer(boolean debugRedraw)
{
- this.debugRedraw=debugRedraw;
+ this.debugRedraw = debugRedraw;
}
public void drawStemAnnot(Graphics g, Annotation[] row_annotations,
@@ -71,18 +78,19 @@ public class AnnotationRenderer
int x2 = (x * charWidth);
Regex closeparen = new Regex("(\\))");
- String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
- : row_annotations[column - 1].displayCharacter;
+ char dc = (column == 0 || row_annotations[column - 1] == null) ? ' '
+ : row_annotations[column - 1].secondaryStructure;
boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
- || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+ || dc != row_annotations[sCol - 1].secondaryStructure;
boolean diffdownstream = !validRes || !validEnd
|| row_annotations[column] == null
- || !dc.equals(row_annotations[column].displayCharacter);
+ || dc != row_annotations[column].secondaryStructure;
// 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 (column > 0 && ResidueProperties.isCloseParenRNA(dc))
{
+
if (diffupstream)
// if (validRes && column>1 && row_annotations[column-2]!=null &&
// dc.equals(row_annotations[column-2].displayCharacter))
@@ -99,6 +107,7 @@ public class AnnotationRenderer
}
else
{
+
// display a forward arrow
if (diffdownstream)
{
@@ -155,23 +164,90 @@ public class AnnotationRenderer
* width of image to render in panel
*/
private int imgWidth;
+
/**
* offset to beginning of visible area
*/
private int sOffset;
+
/**
* offset to end of visible area
*/
private int visHeight;
+
/**
- * indicate if the renderer should only render the visible portion of the annotation given the current view settings
+ * indicate if the renderer should only render the visible portion of the
+ * annotation given the current view settings
*/
- private boolean useClip=true;
+ private boolean useClip = true;
+
/**
- * master flag indicating if renderer should ever try to clip. not enabled for jalview 2.8.1
+ * master flag indicating if renderer should ever try to clip. not enabled for
+ * jalview 2.8.1
*/
- private boolean canClip=false;
-
+ private boolean canClip = false;
+
+ public void drawNotCanonicalAnnot(Graphics g, Color nonCanColor,
+ Annotation[] row_annotations, int lastSSX, int x, int y,
+ int iconOffset, int startRes, int column, boolean validRes,
+ boolean validEnd)
+ {
+ // System.out.println(nonCanColor);
+
+ g.setColor(nonCanColor);
+ int sCol = (lastSSX / charWidth) + startRes;
+ int x1 = lastSSX;
+ int x2 = (x * charWidth);
+ Regex closeparen = new Regex("}|]|<|[a-z]");
+
+ String dc = (column == 0 || row_annotations[column - 1] == null) ? ""
+ : 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))// closeletter_b.search(dc)||closeletter_c.search(dc)||closeletter_d.search(dc)||closecrochet.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);
+ }
+
// public void updateFromAnnotationPanel(FontMetrics annotFM, AlignViewportI
// av)
public void updateFromAwtRenderPanel(AwtRenderPanelI annotPanel,
@@ -182,19 +258,23 @@ public class AnnotationRenderer
fadedImage = annotPanel.getFadedImage();
imgWidth = annotPanel.getFadedImageWidth();
// visible area for rendering
- int[] bounds=annotPanel.getVisibleVRange();
- if (bounds!=null)
+ int[] bounds = annotPanel.getVisibleVRange();
+ if (bounds != null)
{
sOffset = bounds[0];
visHeight = bounds[1];
- if (visHeight==0)
+ if (visHeight == 0)
{
- useClip=false;
- } else {
- useClip=canClip;
+ useClip = false;
+ }
+ else
+ {
+ useClip = canClip;
}
- } else {
- useClip=false;
+ }
+ else
+ {
+ useClip = false;
}
updateFromAlignViewport(av);
@@ -218,6 +298,7 @@ public class AnnotationRenderer
profcolour = av.getAlignment().isNucleotide() ? new jalview.schemes.NucleotideColourScheme()
: new jalview.schemes.ZappoColourScheme();
}
+ boolean rna = av.getAlignment().isNucleotide();
columnSelection = av.getColumnSelection();
hconsensus = av.getSequenceConsensusHash();// hconsensus;
hStrucConsensus = av.getRnaStructureConsensusHash(); // hStrucConsensus;
@@ -274,6 +355,8 @@ public class AnnotationRenderer
return null;
}
+ boolean rna = false;
+
/**
* Render the annotation rows associated with an alignment.
*
@@ -296,7 +379,7 @@ public class AnnotationRenderer
AlignViewportI av, Graphics g, int activeRow, int startRes,
int endRes)
{
- long stime=System.currentTimeMillis();
+ long stime = System.currentTimeMillis();
boolean usedFaded = false;
// NOTES:
// AnnotationPanel needs to implement: ImageObserver, access to
@@ -304,7 +387,8 @@ public class AnnotationRenderer
updateFromAwtRenderPanel(annotPanel, av);
fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- if (aa==null)
+ int temp = 0;
+ if (aa == null)
{
return false;
}
@@ -319,8 +403,10 @@ public class AnnotationRenderer
boolean centreColLabels, centreColLabelsDef = av
.getCentreColumnLabels();
boolean scaleColLabel = false;
- AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation();
- boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
+ AlignmentAnnotation consensusAnnot = av
+ .getAlignmentConsensusAnnotation(), structConsensusAnnot = av
+ .getAlignmentStrucConsensusAnnotation();
+ boolean renderHistogram = true, renderProfile = true, normaliseProfile = false, isRNA = rna;
BitSet graphGroupDrawn = new BitSet();
int charOffset = 0; // offset for a label
@@ -329,13 +415,15 @@ public class AnnotationRenderer
Font ofont = g.getFont();
// \u03B2 \u03B1
// debug ints
- int yfrom=0,f_i=0,yto=0,f_to=0;
- boolean clipst=false,clipend=false;
+ int yfrom = 0, f_i = 0, yto = 0, f_to = 0;
+ boolean clipst = false, clipend = false;
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
+ isRNA = row.isRNA();
{
- // check if this is a consensus annotation row and set the display settings appropriately
+ // check if this is a consensus annotation row and set the display
+ // settings appropriately
// TODO: generalise this to have render styles for consensus/profile
// data
if (row.groupRef != null && row == row.groupRef.getConsensus())
@@ -349,9 +437,12 @@ public class AnnotationRenderer
renderHistogram = av_renderHistogram;
renderProfile = av_renderProfile;
normaliseProfile = av_normaliseProfile;
- } else {
+ }
+ else
+ {
renderHistogram = true;
- // don't need to set render/normaliseProfile since they are not currently used in any other annotation track renderer
+ // don't need to set render/normaliseProfile since they are not
+ // currently used in any other annotation track renderer
}
}
Annotation[] row_annotations = row.annotations;
@@ -364,348 +455,550 @@ public class AnnotationRenderer
scaleColLabel = row.scaleColLabel;
lastSS = ' ';
lastSSX = 0;
-
- if (!useClip || ((y-charHeight)=sOffset))
+
+ if (!useClip
+ || ((y - charHeight) < visHeight && (y + row.height + charHeight * 2) >= sOffset))
{// if_in_visible_region
if (!clipst)
{
- clipst=true;
- yfrom=y;
- f_i=i;
+ clipst = true;
+ yfrom = y;
+ f_i = i;
}
yto = y;
- f_to=i;
- if (row.graph > 0)
- {
- if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup)) {
- continue;
- }
-
- // this is so that we draw the characters below the graph
- y += row.height;
-
- if (row.hasText)
+ f_to = i;
+ if (row.graph > 0)
{
- iconOffset = charHeight - fm.getDescent();
- y -= charHeight;
- }
- }
- else if (row.hasText)
- {
- iconOffset = charHeight - fm.getDescent();
-
- }
- else
- {
- iconOffset = 0;
- }
-
- if (row.autoCalculated && av.isCalculationInProgress(row))
- {
- y += charHeight;
- usedFaded = true;
- g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
- - row.height, imgWidth, y, annotationPanel);
- g.setColor(Color.black);
- // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
+ if (row.graphGroup > -1 && graphGroupDrawn.get(row.graphGroup))
+ {
+ continue;
+ }
- continue;
- }
+ // this is so that we draw the characters below the graph
+ y += row.height;
- /*
- * else if (annotationPanel.av.updatingConservation &&
- * aa[i].label.equals("Conservation")) {
- *
- * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
- * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
- * annotationPanel.imgWidth, y, annotationPanel);
- *
- * g.setColor(Color.black); //
- * g.drawString("Calculating Conservation.....",20, y-row.height/2);
- *
- * continue; } else if (annotationPanel.av.updatingConservation &&
- * aa[i].label.equals("Quality")) {
- *
- * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
- * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
- * annotationPanel.imgWidth, y, annotationPanel); 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 (hasHiddenColumns)
- {
- column = columnSelection.adjustForHiddenColumns(startRes + x);
- if (column > row_annotations.length - 1)
+ if (row.hasText)
{
- break;
+ iconOffset = charHeight - fm.getDescent();
+ y -= charHeight;
}
}
- else
+ else if (row.hasText)
{
- column = startRes + x;
- }
+ iconOffset = charHeight - fm.getDescent();
- if ((row_annotations == null) || (row_annotations.length <= column)
- || (row_annotations[column] == null))
- {
- validRes = false;
}
else
{
- validRes = true;
+ iconOffset = 0;
}
- if (x > -1)
+
+ if (row.autoCalculated && av.isCalculationInProgress(row))
{
- if (activeRow == i)
- {
- g.setColor(Color.red);
+ y += charHeight;
+ usedFaded = true;
+ g.drawImage(fadedImage, 0, y - row.height, imgWidth, y, 0, y
+ - row.height, imgWidth, y, annotationPanel);
+ g.setColor(Color.black);
+ // g.drawString("Calculating "+aa[i].label+"....",20, y-row.height/2);
- if (columnSelection != null)
- {
- for (int n = 0; n < columnSelection.size(); n++)
- {
- int v = columnSelection.columnAt(n);
+ continue;
+ }
- if (v == column)
- {
- g.fillRect(x * charWidth, y, charWidth, charHeight);
- }
- }
+ /*
+ * else if (annotationPanel.av.updatingConservation &&
+ * aa[i].label.equals("Conservation")) {
+ *
+ * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
+ * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
+ * annotationPanel.imgWidth, y, annotationPanel);
+ *
+ * g.setColor(Color.black); //
+ * g.drawString("Calculating Conservation.....",20, y-row.height/2);
+ *
+ * continue; } else if (annotationPanel.av.updatingConservation &&
+ * aa[i].label.equals("Quality")) {
+ *
+ * y += charHeight; g.drawImage(annotationPanel.fadedImage, 0, y -
+ * row.height, annotationPanel.imgWidth, y, 0, y - row.height,
+ * annotationPanel.imgWidth, y, annotationPanel);
+ * 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 (hasHiddenColumns)
+ {
+ column = columnSelection.adjustForHiddenColumns(startRes + x);
+ if (column > row_annotations.length - 1)
+ {
+ break;
}
}
- if (!row.isValidStruc())
+ else
{
- g.setColor(Color.orange);
- g.fillRect((int) row.getInvalidStrucPos() * charWidth, y,
- charWidth, charHeight);
+ column = startRes + x;
}
- if (validCharWidth
- && validRes
- && row_annotations[column].displayCharacter != null
- && (row_annotations[column].displayCharacter.length() > 0))
- {
- if (centreColLabels || scaleColLabel)
+ if ((row_annotations == null)
+ || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
+ {
+ validRes = false;
+ }
+ else
+ {
+ validRes = true;
+ }
+ if (x > -1)
+ {
+ if (activeRow == i)
{
- fmWidth = fm.charsWidth(
- row_annotations[column].displayCharacter
- .toCharArray(), 0,
- row_annotations[column].displayCharacter.length());
+ g.setColor(Color.red);
- if (scaleColLabel)
+ if (columnSelection != null)
{
- // justify the label and scale to fit in column
- if (fmWidth > charWidth)
+ for (int n = 0; n < columnSelection.size(); n++)
{
- // scale only if the current font isn't already small enough
- fmScaling = charWidth;
- fmScaling /= fmWidth;
- g.setFont(ofont.deriveFont(AffineTransform
- .getScaleInstance(fmScaling, 1.0)));
- // and update the label's width to reflect the scaling.
- fmWidth = charWidth;
+ int v = columnSelection.columnAt(n);
+
+ if (v == column)
+ {
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
+ }
}
}
}
- else
+ if (row.getInvalidStrucPos() > x)
{
- fmWidth = fm
- .charWidth(row_annotations[column].displayCharacter
- .charAt(0));
+ g.setColor(Color.orange);
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
}
- charOffset = (int) ((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)
+ else if (row.getInvalidStrucPos() == x)
{
- g.drawString(row_annotations[column].displayCharacter,
- (x * charWidth) + charOffset, y + iconOffset);
+ g.setColor(Color.orange.darker());
+ g.fillRect(x * charWidth, y, charWidth, charHeight);
}
- 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 == ' ')))
+ if (validCharWidth
+ && validRes
+ && row_annotations[column].displayCharacter != null
+ && (row_annotations[column].displayCharacter.length() > 0))
{
- g.drawString(row_annotations[column].displayCharacter, x
- * charWidth + charOffset, y + iconOffset);
+
+ if (centreColLabels || scaleColLabel)
+ {
+ fmWidth = 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 > charWidth)
+ {
+ // scale only if the current font isn't already small enough
+ fmScaling = charWidth;
+ fmScaling /= fmWidth;
+ g.setFont(ofont.deriveFont(AffineTransform
+ .getScaleInstance(fmScaling, 1.0)));
+ // and update the label's width to reflect the scaling.
+ fmWidth = charWidth;
+ }
+ }
+ }
+ else
+ {
+ fmWidth = fm
+ .charWidth(row_annotations[column].displayCharacter
+ .charAt(0));
+ }
+ charOffset = (int) ((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 * 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
+ * charWidth + charOffset, y + iconOffset);
+ }
+ g.setFont(ofont);
}
- g.setFont(ofont);
}
- }
- if (row.hasIcons)
- {
- char ss = validRes ? row_annotations[column].secondaryStructure
- : ' ';
- if (ss == 'S')
+ if (row.hasIcons)
{
- // distinguish between forward/backward base-pairing
- if (row_annotations[column].displayCharacter.indexOf(')') > -1)
+ char ss = validRes ? row_annotations[column].secondaryStructure
+ : '-';
+
+ if (ss == '(')
{
- ss = 's';
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf(')') > -1)
+ {
+
+ ss = ')';
+
+ }
}
- }
- if (!validRes || (ss != lastSS))
- {
- if (x > -1)
+ if (ss == '[')
+ {
+ if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
+ {
+ ss = ']';
+
+ }
+ }
+ if (ss == '{')
{
- switch (lastSS)
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('}') > -1)
{
- case 'H':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
- break;
-
- case 'E':
- drawSheetAnnot(g, row_annotations, 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_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
- break;
-
- default:
- g.setColor(Color.gray);
- g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- - lastSSX, 2);
-
- break;
+ ss = '}';
+
}
}
- if (validRes)
+ if (ss == '<')
{
- lastSS = ss;
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('<') > -1)
+ {
+ ss = '>';
+
+ }
}
- else
+ if (ss >= 65)
{
- lastSS = ' ';
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf(ss + 32) > -1)
+ {
+
+ ss = (char) (ss + 32);
+
+ }
}
- if (x > -1)
+
+ if (!validRes || (ss != lastSS))
{
- lastSSX = (x * charWidth);
+
+ if (x > -1)
+ {
+
+ int nb_annot = x - temp;
+ // System.out.println("\t type :"+lastSS+"\t x :"+x+"\t nbre annot :"+nb_annot);
+ switch (lastSS)
+ {
+ case '(': // Stem case for RNA secondary structure
+ case ')': // and opposite direction
+ drawStemAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes, validEnd);
+ temp = x;
+ break;
+
+ case 'H':
+ if (!isRNA)
+ {
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes,
+ validEnd);
+ break;
+ }
+
+ case 'E':
+ if (!isRNA)
+ {
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y,
+ iconOffset, startRes, column, validRes,
+ validEnd);
+ break;
+ }
+
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'S':
+ case 's':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+
+ Color nonCanColor = getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations,
+ lastSSX, x, y, iconOffset, startRes, column,
+ validRes, validEnd);
+ temp = x;
+ break;
+ default:
+ g.setColor(Color.gray);
+ g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
+ - lastSSX, 2);
+ temp = x;
+ break;
+ }
+ }
+ if (validRes)
+ {
+ lastSS = ss;
+ }
+ else
+ {
+ lastSS = ' ';
+ }
+ if (x > -1)
+ {
+ lastSSX = (x * charWidth);
+ }
}
}
+ column++;
+ x++;
+ }
+ if (column >= row_annotations.length)
+ {
+ column = row_annotations.length - 1;
+ validEnd = false;
+ }
+ else
+ {
+ validEnd = true;
+ }
+ if ((row_annotations == null) || (row_annotations.length <= column)
+ || (row_annotations[column] == null))
+ {
+ validRes = false;
+ }
+ else
+ {
+ validRes = true;
}
- column++;
- x++;
- }
- if (column >= row_annotations.length)
- {
- column = row_annotations.length - 1;
- validEnd = false;
- }
- else
- {
- validEnd = true;
- }
- if ((row_annotations == null) || (row_annotations.length <= column)
- || (row_annotations[column] == null))
- {
- validRes = false;
- }
- else
- {
- validRes = true;
- }
- // x ++;
+ // x ++;
- if (row.hasIcons)
- {
- switch (lastSS)
+ if (row.hasIcons)
{
- case 'H':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
- break;
-
- case 'E':
- drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
- break;
- case 's':
- case 'S': // Stem case for RNA secondary structure
- drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
- break;
- default:
- drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
- break;
+ switch (lastSS)
+ {
+
+ case 'H':
+ if (!isRNA)
+ {
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+ }
+
+ case 'E':
+ if (!isRNA)
+ {
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+ }
+
+ case '(':
+ case ')': // Stem case for RNA secondary structure
+
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+
+ break;
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+ // System.out.println(lastSS);
+ Color nonCanColor = getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX,
+ x, y, iconOffset, startRes, column, validRes, validEnd);
+ break;
+ default:
+ drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset,
+ startRes, column, validRes, validEnd);
+ break;
+ }
}
- }
- if (row.graph > 0 && row.graphHeight > 0)
- {
- if (row.graph == AlignmentAnnotation.LINE_GRAPH)
+ if (row.graph > 0 && row.graphHeight > 0)
{
- if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
+ if (row.graph == AlignmentAnnotation.LINE_GRAPH)
{
- // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels
- float groupmax = -999999, groupmin = 9999999;
- for (int gg = 0; gg < aa.length; gg++)
+ if (row.graphGroup > -1 && !graphGroupDrawn.get(row.graphGroup))
{
- if (aa[gg].graphGroup != row.graphGroup)
+ // TODO: JAL-1291 revise rendering model so the graphGroup map is
+ // computed efficiently for all visible labels
+ float groupmax = -999999, groupmin = 9999999;
+ for (int gg = 0; gg < aa.length; gg++)
{
- continue;
- }
+ 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] != row)
+ {
+ aa[gg].visible = false;
+ }
+ if (aa[gg].graphMax > groupmax)
+ {
+ groupmax = aa[gg].graphMax;
+ }
+ if (aa[gg].graphMin < groupmin)
+ {
+ groupmin = aa[gg].graphMin;
+ }
}
- if (aa[gg].graphMin < groupmin)
+
+ for (int gg = 0; gg < aa.length; gg++)
{
- groupmin = aa[gg].graphMin;
+ if (aa[gg].graphGroup == row.graphGroup)
+ {
+ drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
+ endRes, y, groupmin, groupmax, row.graphHeight);
+ }
}
- }
- for (int gg = 0; gg < aa.length; gg++)
+ graphGroupDrawn.set(row.graphGroup);
+ }
+ else
{
- if (aa[gg].graphGroup == row.graphGroup)
- {
- drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
- endRes, y, groupmin, groupmax, row.graphHeight);
- }
+ drawLineGraph(g, row, row_annotations, startRes, endRes, y,
+ row.graphMin, row.graphMax, row.graphHeight);
}
-
- graphGroupDrawn.set(row.graphGroup);
}
- else
+ else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
- drawLineGraph(g, row, row_annotations, startRes, endRes, y,
- row.graphMin, row.graphMax, row.graphHeight);
+ drawBarGraph(g, row, row_annotations, startRes, endRes,
+ row.graphMin, row.graphMax, y, renderHistogram,
+ renderProfile, normaliseProfile);
}
}
- else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
- {
- drawBarGraph(g, row, row_annotations, startRes, endRes,
- row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile);
- }
}
- } else {
- if (clipst && !clipend)
+ else
{
- clipend = true;
- }
- }// end if_in_visible_region
+ if (clipst && !clipend)
+ {
+ clipend = true;
+ }
+ }// end if_in_visible_region
if (row.graph > 0 && row.hasText)
{
y += charHeight;
@@ -740,13 +1033,15 @@ public class AnnotationRenderer
return !usedFaded;
}
- private final Color GLYPHLINE_COLOR = Color.gray;
+ public static final Color GLYPHLINE_COLOR = Color.gray;
- private final Color SHEET_COLOUR = Color.green;
+ public static final Color SHEET_COLOUR = Color.green;
- private final Color HELIX_COLOUR = Color.red;
+ public static final Color HELIX_COLOUR = Color.red;
- private final Color STEM_COLOUR = Color.blue;
+ public static final Color STEM_COLOUR = Color.blue;
+
+ private Color sdNOTCANONICAL_COLOUR;
public void drawGlyphLine(Graphics g, Annotation[] row, int lastSSX,
int x, int y, int iconOffset, int startRes, int column,
@@ -756,8 +1051,9 @@ public class AnnotationRenderer
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth) - lastSSX, 2);
}
- public void drawSheetAnnot(Graphics g, Annotation[] row, int lastSSX,
- int x, int y, int iconOffset, int startRes, int column,
+ public void drawSheetAnnot(Graphics g, Annotation[] row,
+
+ int lastSSX, int x, int y, int iconOffset, int startRes, int column,
boolean validRes, boolean validEnd)
{
g.setColor(SHEET_COLOUR);
@@ -903,9 +1199,13 @@ public class AnnotationRenderer
}
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);
@@ -933,7 +1233,8 @@ public class AnnotationRenderer
public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, float min,
- float max, int y, boolean renderHistogram,boolean renderProfile,boolean normaliseProfile)
+ float max, int y, boolean renderHistogram, boolean renderProfile,
+ boolean normaliseProfile)
{
if (sRes > aa_annotations.length)
{
@@ -976,9 +1277,13 @@ public class AnnotationRenderer
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);
@@ -1096,9 +1401,13 @@ public class AnnotationRenderer
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)
@@ -1111,4 +1420,131 @@ public class AnnotationRenderer
x += charWidth;
}
}
+
+ Color getNotCanonicalColor(char lastss)
+ {
+ switch (lastss)
+ {
+ case '{':
+ case '}':
+ return new Color(255, 125, 5);
+
+ case '[':
+ case ']':
+ return new Color(245, 115, 10);
+
+ case '>':
+ case '<':
+ return new Color(235, 135, 15);
+
+ case 'A':
+ case 'a':
+ return new Color(225, 105, 20);
+
+ case 'B':
+ case 'b':
+ return new Color(215, 145, 30);
+
+ case 'C':
+ case 'c':
+ return new Color(205, 95, 35);
+
+ case 'D':
+ case 'd':
+ return new Color(195, 155, 45);
+
+ case 'E':
+ case 'e':
+ return new Color(185, 85, 55);
+
+ case 'F':
+ case 'f':
+ return new Color(175, 165, 65);
+
+ case 'G':
+ case 'g':
+ return new Color(170, 75, 75);
+
+ case 'H':
+ case 'h':
+ return new Color(160, 175, 85);
+
+ case 'I':
+ case 'i':
+ return new Color(150, 65, 95);
+
+ case 'J':
+ case 'j':
+ return new Color(140, 185, 105);
+
+ case 'K':
+ case 'k':
+ return new Color(130, 55, 110);
+
+ case 'L':
+ case 'l':
+ return new Color(120, 195, 120);
+
+ case 'M':
+ case 'm':
+ return new Color(110, 45, 130);
+
+ case 'N':
+ case 'n':
+ return new Color(100, 205, 140);
+
+ case 'O':
+ case 'o':
+ return new Color(90, 35, 150);
+
+ case 'P':
+ case 'p':
+ return new Color(85, 215, 160);
+
+ case 'Q':
+ case 'q':
+ return new Color(75, 25, 170);
+
+ case 'R':
+ case 'r':
+ return new Color(65, 225, 180);
+
+ case 'S':
+ case 's':
+ return new Color(55, 15, 185);
+
+ case 'T':
+ case 't':
+ return new Color(45, 235, 195);
+
+ case 'U':
+ case 'u':
+ return new Color(35, 5, 205);
+
+ case 'V':
+ case 'v':
+ return new Color(25, 245, 215);
+
+ case 'W':
+ case 'w':
+ return new Color(15, 0, 225);
+
+ case 'X':
+ case 'x':
+ return new Color(10, 255, 235);
+
+ case 'Y':
+ case 'y':
+ return new Color(5, 150, 245);
+
+ case 'Z':
+ case 'z':
+ return new Color(0, 80, 255);
+
+ default:
+ System.out.println("This is not a interaction : " + lastss);
+ return null;
+
+ }
+ }
}