public ColumnSelection hiddencols;\r
\r
public Vector visibleGroups;\r
+\r
public Hashtable hiddenRepSeqs;\r
- \r
+\r
public ViewDef(String viewname, HiddenSequences hidseqs,\r
ColumnSelection hiddencols, Hashtable hiddenRepSeqs)\r
{\r
refSeq = row.sequenceRef;\r
text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
}\r
+ boolean hasGlyphs = false, hasLabels = false, hasValues = false, hasText = false;\r
+ // lookahead to check what the annotation row object actually contains.\r
+ for (int j = 0; row.annotations != null\r
+ && j < row.annotations.length\r
+ && (!hasGlyphs || !hasLabels || !hasValues); j++)\r
+ {\r
+ if (row.annotations[j] != null)\r
+ {\r
+ hasLabels |= (row.annotations[j].displayCharacter != null\r
+ && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter\r
+ .equals(" "));\r
+ hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' ');\r
+ hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't\r
+ // be\r
+ // rendered..\r
+ hasText |= (row.annotations[j].description != null && row.annotations[j].description\r
+ .length() > 0);\r
+ }\r
+ }\r
\r
if (row.graph == AlignmentAnnotation.NO_GRAPH)\r
{\r
text.append("NO_GRAPH\t");\r
+ hasValues = false; // only secondary structure\r
+ hasLabels = false; // and annotation description string.\r
}\r
else\r
{\r
if (row.graph == AlignmentAnnotation.BAR_GRAPH)\r
{\r
text.append("BAR_GRAPH\t");\r
+ hasGlyphs = false; // no secondary structure\r
+\r
}\r
else if (row.graph == AlignmentAnnotation.LINE_GRAPH)\r
{\r
+ hasGlyphs = false; // no secondary structure\r
text.append("LINE_GRAPH\t");\r
}\r
\r
{\r
text.append(row.description + "\t");\r
}\r
-\r
for (int j = 0; row.annotations != null\r
&& j < row.annotations.length; j++)\r
{\r
if (row.annotations[j] != null)\r
{\r
comma = "";\r
- if (row.annotations[j].secondaryStructure != ' ')\r
+ if (hasGlyphs && row.annotations[j].secondaryStructure != ' ')\r
{\r
+\r
text.append(comma + row.annotations[j].secondaryStructure);\r
comma = ",";\r
}\r
- if (row.annotations[j].displayCharacter != null\r
- && row.annotations[j].displayCharacter.length() > 0\r
- && !row.annotations[j].displayCharacter.equals(" "))\r
+ if (hasValues)\r
{\r
- text.append(comma + row.annotations[j].displayCharacter);\r
+ if (row.annotations[j].value != Float.NaN)\r
+ {\r
+ text.append(comma + row.annotations[j].value);\r
+ }\r
+ else\r
+ {\r
+ System.err.println("Skipping NaN - not valid value.");\r
+ text.append(comma + 0f);// row.annotations[j].value);\r
+ }\r
comma = ",";\r
}\r
-\r
- if (row.annotations[j] != null)\r
+ if (hasLabels)\r
{\r
- if (color != null && !color.equals(row.annotations[j].colour))\r
+ // TODO: labels are emitted after values for bar graphs.\r
+ text.append(comma);\r
+ if // empty labels are allowed, so\r
+ (row.annotations[j].displayCharacter != null\r
+ && row.annotations[j].displayCharacter.length() > 0\r
+ && !row.annotations[j].displayCharacter.equals(" "))\r
{\r
- oneColour = false;\r
+ text.append(comma + row.annotations[j].displayCharacter);\r
+ comma = ",";\r
}\r
-\r
- color = row.annotations[j].colour;\r
- if (row.annotations[j].value != 0f\r
- && row.annotations[j].value != Float.NaN)\r
+ }\r
+ if (hasText)\r
+ {\r
+ if (row.annotations[j].description != null\r
+ && row.annotations[j].description.length() > 0\r
+ && !row.annotations[j].description\r
+ .equals(row.annotations[j].displayCharacter))\r
{\r
- text.append(comma + row.annotations[j].value);\r
+ text.append(comma + row.annotations[j].description);\r
+ comma = ",";\r
}\r
}\r
+ if (color != null && !color.equals(row.annotations[j].colour))\r
+ {\r
+ oneColour = false;\r
+ }\r
+\r
+ color = row.annotations[j].colour;\r
\r
if (row.annotations[j].colour != null\r
&& row.annotations[j].colour != java.awt.Color.black)\r
+ jalview.util.Format\r
.getHexString(row.annotations[j].colour)\r
+ "]");\r
+ comma = ",";\r
}\r
}\r
text.append("|");\r
public void printGroups(Vector sequenceGroups)\r
{\r
SequenceGroup sg;\r
- SequenceI seqrep=null;\r
+ SequenceI seqrep = null;\r
for (int i = 0; i < sequenceGroups.size(); i++)\r
{\r
sg = (SequenceGroup) sequenceGroups.elementAt(i);\r
if (!sg.hasSeqrep())\r
{\r
text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
- + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1) + "\t"\r
- + "-1\t");\r
+ + (sg.getStartRes() + 1) + "\t" + (sg.getEndRes() + 1)\r
+ + "\t" + "-1\t");\r
seqrep = null;\r
- } else {\r
+ }\r
+ else\r
+ {\r
seqrep = sg.getSeqrep();\r
- text.append("SEQUENCE_REF\t"+seqrep.getName()+"\n");\r
+ text.append("SEQUENCE_REF\t" + seqrep.getName() + "\n");\r
text.append("SEQUENCE_GROUP\t" + sg.getName() + "\t"\r
- + (seqrep.findPosition(sg.getStartRes())) + "\t" + (seqrep.findPosition(sg.getEndRes())) + "\t"\r
- + "-1\t");\r
+ + (seqrep.findPosition(sg.getStartRes())) + "\t"\r
+ + (seqrep.findPosition(sg.getEndRes())) + "\t" + "-1\t");\r
}\r
for (int s = 0; s < sg.getSize(); s++)\r
{\r
text.append("displayBoxes=" + sg.getDisplayBoxes() + "\t");\r
text.append("displayText=" + sg.getDisplayText() + "\t");\r
text.append("colourText=" + sg.getColourText() + "\t");\r
- text.append("showUnconserved="+sg.getShowunconserved()+"\t");\r
+ text.append("showUnconserved=" + sg.getShowunconserved() + "\t");\r
if (sg.textColour != java.awt.Color.black)\r
{\r
text.append("textCol1="\r
}\r
if (sg.thresholdTextColour != 0)\r
{\r
- text.append("textColThreshold=" + sg.thresholdTextColour+"\t");\r
+ text.append("textColThreshold=" + sg.thresholdTextColour + "\t");\r
}\r
if (sg.idColour != null)\r
{\r
{\r
text.append("hidecols=true\t");\r
}\r
- if (seqrep!=null)\r
+ if (seqrep != null)\r
{\r
// terminate the last line and clear the sequence ref for the group\r
text.append("\nSEQUENCE_REF");\r
// TODO: verify that undo/redo with 1:many sequence associated\r
// annotations can be undone correctly\r
AlignmentAnnotation ann = new AlignmentAnnotation(annotation);\r
- annotation.createSequenceMapping(referedSeq, refSeqIndex, false);\r
+ annotation\r
+ .createSequenceMapping(referedSeq, refSeqIndex, false);\r
annotation.adjustForAlignment();\r
referedSeq.addAlignmentAnnotation(annotation);\r
al.addAnnotation(annotation);\r
String desc = null, displayChar = null;\r
char ss = ' '; // secondaryStructure\r
float value = 0;\r
- boolean parsedValue = false,dcset=false;\r
+ boolean parsedValue = false, dcset = false;\r
\r
// find colour here\r
java.awt.Color colour = null;\r
if (parsedValue && !dcset)\r
{\r
// allow the value below the bar/line to be empty\r
- dcset=true;\r
- displayChar = "";\r
+ dcset = true;\r
+ displayChar = " ";\r
}\r
continue;\r
}\r
}\r
\r
}\r
-\r
+ if (!dcset && string.charAt(string.length() - 1) == ',')\r
+ {\r
+ displayChar = " "; // empty display char symbol.\r
+ }\r
if (displayChar != null && displayChar.length() > 1 && desc != null\r
&& desc.length() == 1)\r
{\r
\r
annotation.setThreshold(new GraphLine(value, label, colour));\r
}\r
+\r
void addGroup(AlignmentI al, StringTokenizer st)\r
{\r
SequenceGroup sg = new SequenceGroup();\r
sg.setName(st.nextToken());\r
- String rng ="";\r
- try {\r
+ String rng = "";\r
+ try\r
+ {\r
rng = st.nextToken();\r
- if (rng.length()>0 && !rng.startsWith("*"))\r
+ if (rng.length() > 0 && !rng.startsWith("*"))\r
{\r
sg.setStartRes(Integer.parseInt(rng) - 1);\r
- } else {\r
+ }\r
+ else\r
+ {\r
sg.setStartRes(0);\r
}\r
rng = st.nextToken();\r
- if (rng.length()>0 && !rng.startsWith("*"))\r
+ if (rng.length() > 0 && !rng.startsWith("*"))\r
{\r
sg.setEndRes(Integer.parseInt(rng) - 1);\r
- } else {\r
- sg.setEndRes(al.getWidth()-1);\r
+ }\r
+ else\r
+ {\r
+ sg.setEndRes(al.getWidth() - 1);\r
}\r
} catch (Exception e)\r
{\r
- System.err.println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"+rng+"' - assuming alignment width for group.");\r
+ System.err\r
+ .println("Couldn't parse Group Start or End Field as '*' or a valid column or sequence index: '"\r
+ + rng + "' - assuming alignment width for group.");\r
// assume group is full width\r
sg.setStartRes(0);\r
- sg.setEndRes(al.getWidth()-1);\r
+ sg.setEndRes(al.getWidth() - 1);\r
}\r
\r
String index = st.nextToken();\r
git://source.jalview.org / jalview.git / commitdiff