/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
// 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))
}
else
{
+
// display a forward arrow
if (diffdownstream)
{
* master flag indicating if renderer should ever try to clip. not enabled for jalview 2.8.1
*/
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,
}
// TODO extend annotation row to enable dynamic and static profile data to
// be stored
- if (aa.groupRef == null && aa.sequenceRef == null && av_renderProfile)
+ if (aa.groupRef == null && aa.sequenceRef == null)
{
return AAFrequency.extractProfile(hconsensus[column],
av_ignoreGapsConsensus);
// to
// be stored
if (aa.groupRef == null && aa.sequenceRef == null
- && av_renderProfile && hStrucConsensus != null
+ && hStrucConsensus != null
&& hStrucConsensus.length > column)
{
return StructureFrequency.extractProfile(hStrucConsensus[column],
updateFromAwtRenderPanel(annotPanel, av);
fm = g.getFontMetrics();
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ int temp = 0;
if (aa==null)
{
return false;
boolean centreColLabels, centreColLabelsDef = av
.getCentreColumnLabels();
boolean scaleColLabel = false;
+ AlignmentAnnotation consensusAnnot=av.getAlignmentConsensusAnnotation(),structConsensusAnnot=av.getAlignmentStrucConsensusAnnotation();
+ boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
BitSet graphGroupDrawn = new BitSet();
int charOffset = 0; // offset for a label
for (int i = 0; i < aa.length; i++)
{
AlignmentAnnotation row = aa[i];
+ {
+ // 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())
+ {
+ renderHistogram = row.groupRef.isShowConsensusHistogram();
+ renderProfile = row.groupRef.isShowSequenceLogo();
+ normaliseProfile = row.groupRef.isNormaliseSequenceLogo();
+ }
+ else if (row == consensusAnnot || row == structConsensusAnnot)
+ {
+ renderHistogram = av_renderHistogram;
+ renderProfile = av_renderProfile;
+ normaliseProfile = av_normaliseProfile;
+ } else {
+ renderHistogram = true;
+ // don't need to set render/normaliseProfile since they are not currently used in any other annotation track renderer
+ }
+ }
Annotation[] row_annotations = row.annotations;
if (!row.visible)
{
.equals(row_annotations[column - 1].displayCharacter) || (row_annotations[column].displayCharacter
.length() < 2 && row_annotations[column].secondaryStructure == ' ')))
{
- g.drawString(row_annotations[column].displayCharacter, x
+ g.drawString(row_annotations[column].displayCharacter
+ , x
* charWidth + charOffset, y + iconOffset);
}
g.setFont(ofont);
if (row.hasIcons)
{
char ss = validRes ? row_annotations[column].secondaryStructure
- : ' ';
- if (ss == 'S')
+ : '-';
+
+ if (ss == '(')
{
// distinguish between forward/backward base-pairing
if (row_annotations[column].displayCharacter.indexOf(')') > -1)
{
- ss = 's';
+
+ ss = ')';
+
}
}
- if (!validRes || (ss != lastSS))
+ if (ss == '[')
{
- if (x > -1)
+ if ((row_annotations[column].displayCharacter.indexOf(']') > -1))
{
+ ss = ']';
+
+
+ }
+ }
+ if (ss == '{')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('}') > -1)
+ {
+ ss = '}';
+
+
+ }
+ }
+ if (ss == '<')
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf('<') > -1)
+ {
+ ss = '>';
+
+
+ }
+ }
+ if (ss >=65)
+ {
+ // distinguish between forward/backward base-pairing
+ if (row_annotations[column].displayCharacter.indexOf(ss+32) > -1)
+ {
+
+ ss = (char) (ss+32);
+
+
+ }
+ }
+
+
+ if (!validRes || (ss != lastSS))
+ {
+
+
+ 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 'H':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
+ {
+
+ case '$':
+ drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
break;
- case 'E':
- drawSheetAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
+ case 'µ':
+ drawSheetAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
break;
- case 'S': // Stem case for RNA secondary structure
- case 's': // and opposite direction
- drawStemAnnot(g, row_annotations, lastSSX, x, y,
- iconOffset, startRes, column, validRes, validEnd);
+ case '(': // Stem case for RNA secondary structure
+ case ')': // and opposite direction
+ drawStemAnnot(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ temp=x;
break;
-
+ case '{':
+ case '}':
+ case '[':
+ case ']':
+ case '>':
+ case '<':
+ case 'A':
+ case 'a':
+ case 'B':
+ case 'b':
+ case 'C':
+ case 'c':
+ case 'D':
+ case 'd':
+ case 'E':
+ case 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'H':
+ case 'h':
+ case 'I':
+ case 'i':
+ case 'J':
+ case 'j':
+ case 'K':
+ case 'k':
+ case 'L':
+ case 'l':
+ case 'M':
+ case 'm':
+ case 'N':
+ case 'n':
+ case 'O':
+ case 'o':
+ case 'P':
+ case 'p':
+ case 'Q':
+ case 'q':
+ case 'R':
+ case 'r':
+ case 'S':
+ case 's':
+ case 'T':
+ case 't':
+ case 'U':
+ case 'u':
+ case 'V':
+ case 'v':
+ case 'W':
+ case 'w':
+ case 'X':
+ case 'x':
+ case 'Y':
+ case 'y':
+ case 'Z':
+ case 'z':
+
+ Color nonCanColor= getNotCanonicalColor(lastSS);
+ drawNotCanonicalAnnot(g, nonCanColor, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
+ temp=x;
+ break;
default:
g.setColor(Color.gray);
g.fillRect(lastSSX, y + 6 + iconOffset, (x * charWidth)
- lastSSX, 2);
-
+ temp=x;
break;
}
}
{
switch (lastSS)
{
- case 'H':
- drawHelixAnnot(g, row_annotations, lastSSX, x, y, iconOffset,
- startRes, column, validRes, validEnd);
+ case '$':
+ 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);
+ case 'µ':
+ 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);
+
+ 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 'e':
+ case 'F':
+ case 'f':
+ case 'G':
+ case 'g':
+ case 'H':
+ 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);
+ drawGlyphLine(g, row_annotations, lastSSX, x, y, iconOffset, startRes,
+ column, validRes, validEnd);
break;
}
}
{
if (aa[gg].graphGroup == row.graphGroup)
{
- drawLineGraph(g, aa[gg], aa[gg].annotations, startRes,
- endRes, y, groupmin, groupmax, row.graphHeight);
+ drawLineGraph(g, aa[gg], aa[gg].annotations, startRes, endRes, y, groupmin,
+ groupmax, row.graphHeight);
}
}
}
else
{
- drawLineGraph(g, row, row_annotations, startRes, endRes, y,
- row.graphMin, row.graphMax, row.graphHeight);
+ drawLineGraph(g, row, row_annotations, startRes, endRes, y, row.graphMin,
+ row.graphMax, row.graphHeight);
}
}
else if (row.graph == AlignmentAnnotation.BAR_GRAPH)
{
drawBarGraph(g, row, row_annotations, startRes, endRes,
- row.graphMin, row.graphMax, y);
+ row.graphMin, row.graphMax, y, renderHistogram,renderProfile,normaliseProfile);
}
}
} else {
private final Color HELIX_COLOUR = Color.red;
private 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,
- boolean validRes, boolean validEnd)
+ public void drawGlyphLine(Graphics g, Annotation[] row,
+ int lastSSX, int x, int y, int iconOffset, int startRes,
+ int column, boolean validRes, boolean validEnd)
{
g.setColor(GLYPHLINE_COLOR);
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,
- boolean validRes, boolean validEnd)
+ 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);
public void drawBarGraph(Graphics g, AlignmentAnnotation _aa,
Annotation[] aa_annotations, int sRes, int eRes, float min,
- float max, int y)
+ float max, int y, boolean renderHistogram,boolean renderProfile,boolean normaliseProfile)
{
if (sRes > aa_annotations.length)
{
int column;
int aaMax = aa_annotations.length - 1;
- boolean renderHistogram = true, renderProfile = true, normaliseProfile = false;
- // 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();
- normaliseProfile = _aa.groupRef.isNormaliseSequenceLogo();
- }
- else
- {
- renderHistogram = av_renderHistogram;
- renderProfile = av_renderProfile;
- normaliseProfile = av_normaliseProfile;
- }
- }
while (x < eRes - sRes)
{
column = sRes + x;
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;
+
+ }
+ }
}
+
+
+
git://source.jalview.org / jalview.git / blobdiff