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
this.hiddenRepSeqs = hiddenRepSeqs;\r
}\r
}\r
-\r
+ /**\r
+ * Prepare an annotation file given a set of annotations, groups, alignment properties and views. \r
+ * @param annotations\r
+ * @param groups\r
+ * @param properties\r
+ * @param views\r
+ * @return annotation file\r
+ */\r
public String printAnnotations(AlignmentAnnotation[] annotations,\r
Vector groups, Hashtable properties, ViewDef[] views)\r
{\r
+ // TODO: resolve views issue : annotationFile could contain visible region, or full data + hidden region specifications for a view.\r
if (annotations != null)\r
{\r
boolean oneColour = true;\r
\r
StringBuffer colours = new StringBuffer();\r
StringBuffer graphLine = new StringBuffer();\r
-\r
+ StringBuffer rowprops = new StringBuffer();\r
Hashtable graphGroup = new Hashtable();\r
\r
java.awt.Color color;\r
refSeq = row.sequenceRef;\r
text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
}\r
+ boolean hasGlyphs = row.hasIcons, hasLabels = row.hasText, hasValues = row.hasScore, 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) // could be also hasGlyphs || ... \r
{\r
- text.append(comma + row.annotations[j].secondaryStructure);\r
+\r
+ text.append(comma);\r
+ if (row.annotations[j].secondaryStructure != ' ')\r
+ {\r
+ // only write out the field if its not whitespace.\r
+ text.append(row.annotations[j].secondaryStructure);\r
+ }\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
+ 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
colours.append("COLOUR\t" + row.label + "\t"\r
+ jalview.util.Format.getHexString(color) + "\n");\r
}\r
-\r
+ if (row.scaleColLabel || row.showAllColLabels || row.centreColLabels)\r
+ {\r
+ rowprops.append("ROWPROPERTIES\t"+row.label);\r
+ rowprops.append("\tscaletofit="+row.scaleColLabel);\r
+ rowprops.append("\tshowalllabs="+row.showAllColLabels);\r
+ rowprops.append("\tcentrelabs="+row.centreColLabels);\r
+ rowprops.append("\n");\r
+ }\r
}\r
\r
text.append("\n");\r
text.append(en.nextElement() + "\n");\r
}\r
}\r
+ text.append(rowprops.toString());\r
}\r
\r
if (groups != null)\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
public boolean readAnnotationFile(AlignmentI al, String file,\r
String protocol)\r
{\r
+ Hashtable autoAnnots=new Hashtable();\r
try\r
{\r
BufferedReader in = null;\r
int graphStyle, index;\r
int refSeqIndex = 1;\r
int existingAnnotations = 0;\r
+ // when true - will add new rows regardless of whether they are duplicate auto-annotation like consensus or conservation graphs\r
+ boolean overrideAutoAnnot=false; \r
if (al.getAlignmentAnnotation() != null)\r
{\r
existingAnnotations = al.getAlignmentAnnotation().length;\r
+ if (existingAnnotations>0)\r
+ {\r
+ AlignmentAnnotation[] aa = al.getAlignmentAnnotation();\r
+ for (int aai=0;aai<aa.length;aai++)\r
+ {\r
+ if (aa[aai].autoCalculated)\r
+ {\r
+ // make a note of the name and description\r
+ autoAnnots.put(aa[aai].graph+"\t"+aa[aai].label+"\t"+aa[aai].description+"\t"+(aa[aai].sequenceRef!=null ? aa[aai].sequenceRef.getDisplayId(true) : "")\r
+ ,new Integer(1));\r
+ }\r
+ }\r
+ }\r
}\r
\r
int alWidth = al.getWidth();\r
combineAnnotations(al, st);\r
continue;\r
}\r
-\r
+ else if (token.equalsIgnoreCase("ROWPROPERTIES"))\r
+ {\r
+ addRowProperties(al, st);\r
+ continue;\r
+ }\r
else if (token.equalsIgnoreCase("GRAPHLINE"))\r
{\r
addLine(al, st);\r
}\r
else\r
{\r
- annotations[index++] = parseAnnotation(token);\r
+ annotations[index++] = parseAnnotation(token, graphStyle);\r
emptyColumn = false;\r
}\r
}\r
\r
}\r
-\r
+ \r
annotation = new AlignmentAnnotation(label, description,\r
(index == 0) ? null : annotations, 0, 0, graphStyle);\r
\r
annotation.score = score;\r
-\r
+ if (!overrideAutoAnnot && autoAnnots.containsKey(annotation.graph+"\t"+annotation.label+"\t"+annotation.description+"\t"+(refSeq!=null ? refSeq.getDisplayId(true) : "")))\r
+ {\r
+ // skip - we've already got an automatic annotation of this type.\r
+ continue;\r
+ }\r
+ // otherwise add it!\r
if (refSeq != null)\r
{\r
+ \r
annotation.belowAlignment = false;\r
// make a copy of refSeq so we can find other matches in the alignment\r
SequenceI referedSeq = refSeq;\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
return true;\r
}\r
\r
- Annotation parseAnnotation(String string)\r
+ Annotation parseAnnotation(String string, int graphStyle)\r
{\r
+ boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't do the glyph test if we don't want secondary structure\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
UserColourScheme ucs = new UserColourScheme();\r
\r
colour = ucs.getColourFromString(string.substring(i + 1, j));\r
-\r
+ if ( i>0 && string.charAt(i-1)==',')\r
+ {\r
+ // clip the preceding comma as well\r
+ i--;\r
+ }\r
string = string.substring(0, i) + string.substring(j + 1);\r
}\r
\r
- StringTokenizer st = new StringTokenizer(string, ",");\r
+ StringTokenizer st = new StringTokenizer(string, ",", true);\r
String token;\r
+ boolean seenContent=false;\r
+ int pass=0;\r
while (st.hasMoreTokens())\r
{\r
+ pass++;\r
token = st.nextToken().trim();\r
- if (token.length() == 0)\r
+ if (token.equals(","))\r
{\r
- if (parsedValue && !dcset)\r
+ if (!seenContent && 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
+ seenContent = false;\r
continue;\r
+ } else {\r
+ seenContent = true;\r
}\r
\r
if (!parsedValue)\r
{\r
try\r
{\r
- displayChar = token;\r
+ displayChar = token; \r
+ // foo\r
value = new Float(token).floatValue();\r
parsedValue = true;\r
continue;\r
} catch (NumberFormatException ex)\r
{\r
}\r
+ } else {\r
+ if (token.length()==1)\r
+ {\r
+ displayChar = token;\r
+ }\r
}\r
-\r
- if (token.equals("H") || token.equals("E"))\r
+ if (hasSymbols && (token.equals("H") || token.equals("E") || token.equals(" ")))\r
{\r
// Either this character represents a helix or sheet\r
// or an integer which can be displayed\r
displayChar = "";\r
}\r
}\r
- else if (desc == null)\r
+ else if (desc == null || (parsedValue && pass>2))\r
{\r
desc = token;\r
}\r
\r
}\r
-\r
- if (displayChar != null && displayChar.length() > 1 && desc != null\r
- && desc.length() == 1)\r
+// if (!dcset && string.charAt(string.length() - 1) == ',')\r
+// {\r
+// displayChar = " "; // empty display char symbol.\r
+// }\r
+ if (displayChar != null && desc!=null && desc.length()==1) \r
{\r
- String tmp = displayChar;\r
- displayChar = desc;\r
- desc = tmp;\r
+ if (displayChar.length() > 1)\r
+ {\r
+ // switch desc and displayChar - legacy support \r
+ String tmp = displayChar;\r
+ displayChar = desc;\r
+ desc = tmp;\r
+ } else {\r
+ if (displayChar.equals(desc)) {\r
+ // duplicate label - hangover from the 'robust parser' above\r
+ desc = null;\r
+ }\r
+ }\r
}\r
- /*\r
- * In principle, this code will ensure that the Annotation element generated\r
- * is renderable by any of the applet or application rendering code but\r
- * instead we check for null strings when the display character is rendered.\r
- * if (displayChar==null) { displayChar=""; }\r
- */\r
Annotation anot = new Annotation(displayChar, desc, ss, value);\r
\r
anot.colour = colour;\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
}\r
}\r
\r
+ void addRowProperties(AlignmentI al, StringTokenizer st)\r
+ {\r
+ String label = st.nextToken(),keyValue,key,value;\r
+ boolean scaletofit=false,centerlab=false,showalllabs=false;\r
+ while (st.hasMoreTokens()) {\r
+ keyValue=st.nextToken();\r
+ key = keyValue.substring(0, keyValue.indexOf("="));\r
+ value = keyValue.substring(keyValue.indexOf("=") + 1);\r
+ if (key.equalsIgnoreCase("scaletofit")) {\r
+ scaletofit = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ if (key.equalsIgnoreCase("showalllabs")) {\r
+ showalllabs = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ if (key.equalsIgnoreCase("centrelabs")) {\r
+ centerlab = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ AlignmentAnnotation[] alr = al.getAlignmentAnnotation(); \r
+ for (int i = 0; i < alr.length; i++)\r
+ {\r
+ if (alr[i].label.equalsIgnoreCase(label))\r
+ {\r
+ alr[i].centreColLabels = centerlab;\r
+ alr[i].scaleColLabel = scaletofit;\r
+ alr[i].showAllColLabels = showalllabs;\r
+ }\r
+ }\r
+ }\r
+ }\r
void addProperties(AlignmentI al, StringTokenizer st)\r
{\r
\r
git://source.jalview.org / jalview.git / blobdiff