import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DynamicData;
+import jalview.datamodel.DynamicData.DataType;
import jalview.datamodel.GraphLine;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.HiddenSequences;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
import java.awt.Color;
import java.io.BufferedReader;
+import java.io.File;
import java.io.FileReader;
import java.io.InputStreamReader;
import java.io.StringReader;
public class AnnotationFile
{
+ StringBuffer text;
+
+ SequenceI refSeq = null;
+
+ String refSeqId = null;
+
+ String[] StructModelHeader = null;
+
+ long nlinesread = 0;
+
+ String lastread = "";
+
+ /**
+ * used for resolving absolute references to resources relative to
+ * annotationFile location
+ */
+ String baseUri = "";
+
+ private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE",
+ STRUCTMODEL = "STRUCTMODEL",
+ HEADER_STRUCT_MODEL = "HEADER_STRUCT_MODEL";
+
public AnnotationFile()
{
init();
return newline;
}
- StringBuffer text;
private void init()
{
}
}
- SequenceI refSeq = null;
-
- String refSeqId = null;
public boolean annotateAlignmentView(AlignViewportI viewport,
String file, DataSourceType protocol)
public boolean readAnnotationFile(AlignmentI al, HiddenColumns hidden,
String file, DataSourceType sourceType)
{
+ baseUri = "";
BufferedReader in = null;
try
{
if (sourceType == DataSourceType.FILE)
{
in = new BufferedReader(new FileReader(file));
+ baseUri = new File(file).getParent();
+ if (baseUri == null)
+ {
+ baseUri = "";
+ }
+ else
+ {
+ baseUri += "/";
+ }
}
else if (sourceType == DataSourceType.URL)
{
URL url = new URL(file);
in = new BufferedReader(new InputStreamReader(url.openStream()));
+ String bs = url.toExternalForm();
+ baseUri = bs.substring(0, bs.indexOf(url.getHost())
+ + url.getHost().length());
+ baseUri += url.toURI().getPath();
+ if (baseUri.lastIndexOf("/") > -1)
+ {
+ baseUri = baseUri.substring(0, baseUri.lastIndexOf("/")) + "/";
+ }
}
else if (sourceType == DataSourceType.PASTE)
{
in = new BufferedReader(new StringReader(file));
+ // TODO - support mimencoded PDBs for a paste.. ?
+ baseUri = "";
}
else if (sourceType == DataSourceType.CLASSLOADER)
{
if (is != null)
{
in = new BufferedReader(new java.io.InputStreamReader(is));
+ // TODO: this probably doesn't work for classloader - needs a test
+ baseUri = new File("/" + file).getParent() + "/";
}
}
if (in != null)
return false;
}
- long nlinesread = 0;
-
- String lastread = "";
-
- private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,
BufferedReader in) throws Exception
modified = true;
continue;
}
- // else if (token.equalsIgnoreCase("VIEW_DEF"))
- // {
- // addOrSetView(al,st);
- // modified = true;
- // continue;
- // }
else if (token.equalsIgnoreCase("VIEW_SETREF"))
{
if (refSeq != null)
modified = true;
continue;
}
-
+ else if (token.equalsIgnoreCase(HEADER_STRUCT_MODEL))
+ {
+ int hSize = st.countTokens();
+ StructModelHeader = new String[hSize];
+ for (int x = 0; x < hSize; x++)
+ {
+ StructModelHeader[x] = st.nextToken();
+ }
+ continue;
+ }
+ else if (token.equalsIgnoreCase(STRUCTMODEL))
+ {
+ boolean failedtoadd = true;
+ // expects STRUCTMODEL <Query> <TemplateSeqId> <ModelFile>
+ // <FastaMappingFile>
+ String querySeqId = !st.hasMoreTokens() ? "" : st.nextToken();
+ SequenceI querySeq = al.findName(querySeqId);
+ if (st.hasMoreTokens()) {
+ refSeq = al.findName(refSeqId = st.nextToken());
+ if (refSeq == null)
+ {
+ System.err.println("Couldn't locate " + refSeqId
+ + " in the alignment for STRUCTMODEL");
+ refSeqId = null;
+ }
+ else
+ {
+ int tSize = st.countTokens() + 2;
+ String[] rowData = new String[tSize];
+ rowData[0] = querySeqId;
+ rowData[1] = refSeqId;
+ for (int x = 2; x < tSize; x++)
+ {
+ rowData[x] = st.nextToken();
+ }
+ if (processStructModel(al, querySeq, refSeq,
+ StructModelHeader, rowData, baseUri))
+ {
+ failedtoadd = false;
+ }
+ }
+ }
+ if (failedtoadd)
+ {
+ System.err
+ .println("Need minimum of <Query> <TemplateSeqId> <ModelFile> <FastaMappingFile> as tab separated fields after"
+ + STRUCTMODEL);
+ } else {
+ modified = true;
+ }
+ continue;
+ }
// Parse out the annotation row
graphStyle = AlignmentAnnotation.getGraphValueFromString(token);
label = st.nextToken();
return modified;
}
+
+ /**
+ * Resolve structural model to a reference sequence and register it to
+ * StructureSelectionManager
+ *
+ * @param al
+ * @param querySequence
+ * @param templateSeq
+ * @param structModelHeader
+ * @param structModelData
+ * @return true if model and sequence was added
+ */
+ static boolean processStructModel(AlignmentI al, SequenceI querySequence,
+ SequenceI templateSeq,
+ String[] structModelHeader,
+ String[] structModelData, String baseUri)
+ {
+ String warningMessage = null;
+ boolean added = false;
+ try {
+ String structureModelFile = resolveAbsolutePath(structModelData[2],
+ baseUri);
+ String fastaMappingFile = resolveAbsolutePath(structModelData[3],
+ baseUri);
+ // System.out.println("Model File >> " + structureModelFile);
+ // System.out.println("Fasta File >> " + fastaMappingFile);
+ String modelName = StructureFile.safeName(structureModelFile);
+ PDBEntry phyre2PDBEntry = new PDBEntry(modelName, " ",
+ Type.PDB,
+ structureModelFile);
+ List<DynamicData> phyreDD = generatePhyreDynamicDataList(
+ structModelHeader, structModelData);
+ phyre2PDBEntry.setProperty("DYNAMIC_DATA_PHYRE2", phyreDD);
+ templateSeq.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ if (querySequence != null)
+ {
+ querySequence.getDatasetSequence().addPDBId(phyre2PDBEntry);
+ }
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager();
+ ssm.registerPhyre2Template(structureModelFile, fastaMappingFile);
+ added = true;
+
+ } catch (Exception x)
+ {
+ warningMessage = x.toString();
+ } finally {
+ if (warningMessage !=null)
+ {
+ System.err.println("Warnings whilst processing STRUCTMODEL: "+warningMessage);
+ }
+ }
+ return added;
+ }
+
+ static List<DynamicData> generatePhyreDynamicDataList(
+ String[] headerArray,
+ String[] dataArray)
+ {
+
+ if (headerArray == null || dataArray == null)
+ {
+ throw new IllegalArgumentException(
+ "Header or data arrays must not be null");
+ }
+
+ if (headerArray.length != dataArray.length)
+ {
+ throw new IllegalArgumentException(
+ "Header and data arrays must be of same lenght");
+ }
+ List<DynamicData> dynamicDataList = new ArrayList<DynamicData>();
+ int x = 0;
+ for (String data : dataArray)
+ {
+ // first four column should be hidden;
+ boolean show = (x > 4);
+ dynamicDataList.add(new DynamicData(headerArray[x], data, DataType.S,
+ "PHYRE2", show));
+ x++;
+ }
+ return dynamicDataList;
+ }
+
+ static String resolveAbsolutePath(String relURI, String _baseUri)
+ {
+ if (relURI.indexOf(":/") > -1 || relURI.startsWith("/")
+ || "".equals(_baseUri) || relURI.startsWith(_baseUri))
+ {
+ return relURI;
+ }
+ return _baseUri + relURI;
+ }
+
private void parseHideCols(HiddenColumns hidden, String nextToken)
{
StringTokenizer inval = new StringTokenizer(nextToken, ",");
git://source.jalview.org / jalview.git / blobdiff