/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
* \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
* \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.io;\r
\r
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
}\r
}\r
\r
+ /**\r
+ * Prepare an annotation file given a set of annotations, groups, alignment\r
+ * properties and views.\r
+ * \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,\r
+ // or full data + hidden region specifications for a view.\r
if (annotations != null)\r
{\r
boolean oneColour = true;\r
AlignmentAnnotation row;\r
String comma;\r
SequenceI refSeq = null;\r
+ SequenceGroup refGroup = null;\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 = null;\r
}\r
\r
- else if (refSeq == null || refSeq != row.sequenceRef)\r
+ else\r
{\r
- refSeq = row.sequenceRef;\r
- text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
+ if (refSeq == null || refSeq != row.sequenceRef)\r
+ {\r
+ refSeq = row.sequenceRef;\r
+ text.append("\nSEQUENCE_REF\t" + refSeq.getName() + "\n");\r
+ }\r
+ }\r
+ // mark any group references for the row\r
+ if (row.groupRef == null)\r
+ {\r
+\r
+ if (refGroup != null)\r
+ {\r
+ text.append("\nGROUP_REF\tALIGNMENT\n");\r
+ }\r
+\r
+ refGroup = null;\r
+ }\r
+ else\r
+ {\r
+ if (refGroup == null || refGroup != row.groupRef)\r
+ {\r
+ refGroup = row.groupRef;\r
+ text.append("\nGROUP_REF\t" + refGroup.getName() + "\n");\r
+ }\r
+ }\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\r
+ || 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.getShowNonconserved() + "\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
+ String groupRef = null;\r
+ Hashtable groupRefRows = new Hashtable();\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\r
+ // 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\r
+ + "\t"\r
+ + aa[aai].label\r
+ + "\t"\r
+ + aa[aai].description\r
+ + "\t"\r
+ + (aa[aai].sequenceRef != null ? aa[aai].sequenceRef\r
+ .getDisplayId(true) : ""), new Integer(1));\r
+ }\r
+ }\r
+ }\r
}\r
\r
int alWidth = al.getWidth();\r
token = st.nextToken();\r
if (token.equalsIgnoreCase("COLOUR"))\r
{\r
+ // TODO: use graduated colour def'n here too\r
colourAnnotations(al, st.nextToken(), st.nextToken());\r
continue;\r
}\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
continue;\r
}\r
-\r
+ else if (token.equalsIgnoreCase("GROUP_REF"))\r
+ {\r
+ // Group references could be forward or backwards, so they are\r
+ // resolved after the whole file is read in\r
+ groupRef = null;\r
+ if (st.hasMoreTokens())\r
+ {\r
+ groupRef = st.nextToken();\r
+ if (groupRef.length() < 1)\r
+ {\r
+ groupRef = null; // empty string\r
+ }\r
+ else\r
+ {\r
+ if (groupRefRows.get(groupRef) == null)\r
+ {\r
+ groupRefRows.put(groupRef, new Vector());\r
+ }\r
+ }\r
+ }\r
+ continue;\r
+ }\r
else if (token.equalsIgnoreCase("SEQUENCE_GROUP"))\r
{\r
addGroup(al, st);\r
continue;\r
}\r
\r
+ // Parse out the annotation row\r
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);\r
label = st.nextToken();\r
\r
}\r
else\r
{\r
- annotations[index++] = parseAnnotation(token);\r
+ annotations[index++] = parseAnnotation(token, graphStyle);\r
emptyColumn = false;\r
}\r
}\r
(index == 0) ? null : annotations, 0, 0, graphStyle);\r
\r
annotation.score = score;\r
-\r
+ if (!overrideAutoAnnot\r
+ && autoAnnots\r
+ .containsKey(annotation.graph\r
+ + "\t"\r
+ + annotation.label\r
+ + "\t"\r
+ + annotation.description\r
+ + "\t"\r
+ + (refSeq != null ? refSeq\r
+ .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
al.setAnnotationIndex(annotation,\r
al.getAlignmentAnnotation().length\r
- existingAnnotations - 1);\r
+ if (groupRef != null)\r
+ {\r
+ ((Vector) groupRefRows.get(groupRef)).addElement(annotation);\r
+ }\r
// and recover our virgin copy to use again if necessary.\r
annotation = ann;\r
\r
al.setAnnotationIndex(annotation,\r
al.getAlignmentAnnotation().length - existingAnnotations\r
- 1);\r
+ if (groupRef != null)\r
+ {\r
+ ((Vector) groupRefRows.get(groupRef)).addElement(annotation);\r
+ }\r
}\r
}\r
+ // Finally, resolve the groupRefs\r
+ Enumeration en = groupRefRows.keys();\r
+ SequenceGroup theGroup = null;\r
\r
+ while (en.hasMoreElements())\r
+ {\r
+ groupRef = (String) en.nextElement();\r
+ boolean matched = false;\r
+ // Resolve group: TODO: add a getGroupByName method to alignments\r
+ Vector grps = al.getGroups();\r
+ for (int g = 0, gSize = grps.size(); g < gSize; g++)\r
+ {\r
+ theGroup = (SequenceGroup) grps.elementAt(g);\r
+ if (theGroup.getName().equals(groupRef))\r
+ {\r
+ if (matched)\r
+ {\r
+ // TODO: specify and implement duplication of alignment annotation\r
+ // for multiple group references.\r
+ System.err\r
+ .println("Ignoring 1:many group reference mappings for group name '"\r
+ + groupRef + "'");\r
+ }\r
+ else\r
+ {\r
+ matched = true;\r
+ Vector rowset = (Vector) groupRefRows.get(groupRef);\r
+ if (rowset != null && rowset.size() > 0)\r
+ {\r
+ AlignmentAnnotation alan = null;\r
+ for (int elm = 0, elmSize = rowset.size(); elm < elmSize; elm++)\r
+ {\r
+ alan = (AlignmentAnnotation) rowset.elementAt(elm);\r
+ alan.groupRef = theGroup;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ ((Vector) groupRefRows.get(groupRef)).removeAllElements();\r
+ }\r
} catch (Exception ex)\r
{\r
ex.printStackTrace();\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\r
+ // do the\r
+ // glyph\r
+ // test\r
+ // if we\r
+ // don't\r
+ // want\r
+ // secondary\r
+ // structure\r
String desc = null, displayChar = null;\r
char ss = ' '; // secondaryStructure\r
float value = 0;\r
- boolean parsedValue = 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 (!seenContent && parsedValue && !dcset)\r
+ {\r
+ // allow the value below the bar/line to be empty\r
+ dcset = true;\r
+ displayChar = " ";\r
+ }\r
+ seenContent = false;\r
continue;\r
}\r
+ else\r
+ {\r
+ seenContent = true;\r
+ }\r
\r
if (!parsedValue)\r
{\r
try\r
{\r
displayChar = token;\r
+ // foo\r
value = new Float(token).floatValue();\r
parsedValue = true;\r
continue;\r
{\r
}\r
}\r
-\r
- if (token.equals("H") || token.equals("E"))\r
+ else\r
+ {\r
+ if (token.length() == 1)\r
+ {\r
+ displayChar = token;\r
+ }\r
+ }\r
+ if (hasSymbols\r
+ && (token.equals("H") || token.equals("E") || token\r
+ .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
+ }\r
+ else\r
+ {\r
+ if (displayChar.equals(desc))\r
+ {\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
int graphGroup = -1;\r
String group = st.nextToken();\r
// First make sure we are not overwriting the graphIndex\r
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
- {\r
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
- {\r
- graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;\r
- al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
- break;\r
- }\r
- }\r
-\r
- // Now update groups\r
- while (st.hasMoreTokens())\r
+ if (al.getAlignmentAnnotation() != null)\r
{\r
- group = st.nextToken();\r
for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
{\r
if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
{\r
+ graphGroup = al.getAlignmentAnnotation()[i].graphGroup + 1;\r
al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
break;\r
}\r
}\r
+\r
+ // Now update groups\r
+ while (st.hasMoreTokens())\r
+ {\r
+ group = st.nextToken();\r
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
+ {\r
+ if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
+ {\r
+ al.getAlignmentAnnotation()[i].graphGroup = graphGroup;\r
+ break;\r
+ }\r
+ }\r
+ }\r
+ }\r
+ else\r
+ {\r
+ System.err\r
+ .println("Couldn't combine annotations. None are added to alignment yet!");\r
}\r
}\r
\r
void addLine(AlignmentI al, StringTokenizer st)\r
{\r
String group = st.nextToken();\r
- AlignmentAnnotation annotation = null;\r
-\r
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
+ AlignmentAnnotation annotation = null, alannot[] = al\r
+ .getAlignmentAnnotation();\r
+ if (alannot != null)\r
{\r
- if (al.getAlignmentAnnotation()[i].label.equalsIgnoreCase(group))\r
+ for (int i = 0; i < alannot.length; i++)\r
{\r
- annotation = al.getAlignmentAnnotation()[i];\r
- break;\r
+ if (alannot[i].label.equalsIgnoreCase(group))\r
+ {\r
+ annotation = alannot[i];\r
+ break;\r
+ }\r
}\r
}\r
-\r
if (annotation == null)\r
{\r
return;\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
+ {\r
+ keyValue = st.nextToken();\r
+ key = keyValue.substring(0, keyValue.indexOf("="));\r
+ value = keyValue.substring(keyValue.indexOf("=") + 1);\r
+ if (key.equalsIgnoreCase("scaletofit"))\r
+ {\r
+ scaletofit = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ if (key.equalsIgnoreCase("showalllabs"))\r
+ {\r
+ showalllabs = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ if (key.equalsIgnoreCase("centrelabs"))\r
+ {\r
+ centerlab = Boolean.valueOf(value).booleanValue();\r
+ }\r
+ AlignmentAnnotation[] alr = al.getAlignmentAnnotation();\r
+ if (alr != null)\r
+ {\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
+ }\r
+\r
void addProperties(AlignmentI al, StringTokenizer st)\r
{\r
\r
}\r
else if (key.equalsIgnoreCase("showUnconserved"))\r
{\r
- sg.setShowunconserved(Boolean.valueOf(value).booleanValue());\r
+ sg.setShowNonconserved(Boolean.valueOf(value).booleanValue());\r
}\r
else if (key.equalsIgnoreCase("displayText"))\r
{\r
void setBelowAlignment(AlignmentI al, StringTokenizer st)\r
{\r
String token;\r
- AlignmentAnnotation aa;\r
+ AlignmentAnnotation aa, ala[] = al.getAlignmentAnnotation();\r
+ if (ala == null)\r
+ {\r
+ System.err\r
+ .print("Warning - no annotation to set below for sequence associated annotation:");\r
+ }\r
while (st.hasMoreTokens())\r
{\r
token = st.nextToken();\r
- for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
+ if (ala == null)\r
+ {\r
+ System.err.print(" "+token);\r
+ }\r
+ else\r
{\r
- aa = al.getAlignmentAnnotation()[i];\r
- if (aa.sequenceRef == refSeq && aa.label.equals(token))\r
+ for (int i = 0; i < al.getAlignmentAnnotation().length; i++)\r
{\r
- aa.belowAlignment = true;\r
+ aa = al.getAlignmentAnnotation()[i];\r
+ if (aa.sequenceRef == refSeq && aa.label.equals(token))\r
+ {\r
+ aa.belowAlignment = true;\r
+ }\r
}\r
}\r
}\r
+ if (ala==null)\r
+ {\r
+ System.err.print("\n");\r
+ }\r
}\r
\r
void addAlignmentDetails(AlignmentI al, StringTokenizer st)\r
git://source.jalview.org / jalview.git / blobdiff