X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=49e99a105ae5703c6e8656c71b536e63e7546b35;hb=c51dbe7933683b64548f5353e67561d2b5e377f7;hp=2af3fcd8cf607271260a232929cab33fe9aa81fd;hpb=d15f5de72b92c8ac1b217362dc565c496e8f9370;p=jalview.git

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 2af3fcd..49e99a1 100755
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -26,17 +26,23 @@ import jalview.datamodel.AlignmentAnnotation;
 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.schemes.UserColourScheme;
+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;
@@ -52,6 +58,28 @@ import java.util.Vector;
 
 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();
@@ -78,7 +106,6 @@ public class AnnotationFile
     return newline;
   }
 
-  StringBuffer text;
 
   private void init()
   {
@@ -110,23 +137,22 @@ public class AnnotationFile
    */
   public class ViewDef
   {
-    public String viewname;
+    // TODO this class is not used - remove?
+    public final String viewname;
 
-    public HiddenSequences hidseqs;
+    public final HiddenSequences hidseqs;
 
-    public ColumnSelection hiddencols;
+    public final HiddenColumns hiddencols;
 
-    public Vector visibleGroups;
+    public final Hashtable hiddenRepSeqs;
 
-    public Hashtable hiddenRepSeqs;
-
-    public ViewDef(String viewname, HiddenSequences hidseqs,
-            ColumnSelection hiddencols, Hashtable hiddenRepSeqs)
+    public ViewDef(String vname, HiddenSequences hseqs,
+            HiddenColumns hcols, Hashtable hRepSeqs)
     {
-      this.viewname = viewname;
-      this.hidseqs = hidseqs;
-      this.hiddencols = hiddencols;
-      this.hiddenRepSeqs = hiddenRepSeqs;
+      this.viewname = vname;
+      this.hidseqs = hseqs;
+      this.hiddencols = hcols;
+      this.hiddenRepSeqs = hRepSeqs;
     }
   }
 
@@ -142,7 +168,8 @@ public class AnnotationFile
    */
   public String printAnnotations(AlignmentAnnotation[] annotations,
           List<SequenceGroup> list, Hashtable properties,
-          ColumnSelection cs, AlignmentI al, ViewDef view)
+ HiddenColumns cs,
+          AlignmentI al, ViewDef view)
   {
     if (view != null)
     {
@@ -152,7 +179,7 @@ public class AnnotationFile
       }
       if (list == null)
       {
-        list = view.visibleGroups;
+        // list = view.visibleGroups;
       }
       if (cs == null)
       {
@@ -171,7 +198,7 @@ public class AnnotationFile
     if (cs != null && cs.hasHiddenColumns())
     {
       text.append("VIEW_HIDECOLS\t");
-      List<int[]> hc = cs.getHiddenColumns();
+      List<int[]> hc = cs.getHiddenRegions();
       boolean comma = false;
       for (int[] r : hc)
       {
@@ -537,7 +564,7 @@ public class AnnotationFile
     return false;
   }
 
-  public void printGroups(List<SequenceGroup> list)
+  protected void printGroups(List<SequenceGroup> list)
   {
     SequenceI seqrep = null;
     for (SequenceGroup sg : list)
@@ -583,7 +610,8 @@ public class AnnotationFile
       if (sg.cs != null)
       {
         text.append("colour=");
-        text.append(sg.cs.toString());
+        text.append(ColourSchemeProperty.getColourName(sg.cs
+                .getColourScheme()));
         text.append("\t");
         if (sg.cs.getThreshold() != 0)
         {
@@ -657,23 +685,26 @@ public class AnnotationFile
     }
   }
 
-  SequenceI refSeq = null;
-
-  String refSeqId = null;
 
   public boolean annotateAlignmentView(AlignViewportI viewport,
           String file, DataSourceType protocol)
   {
     ColumnSelection colSel = viewport.getColumnSelection();
+    HiddenColumns hidden = viewport.getAlignment().getHiddenColumns();
     if (colSel == null)
     {
       colSel = new ColumnSelection();
     }
-    boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel,
+    if (hidden == null)
+    {
+      hidden = new HiddenColumns();
+    }
+    boolean rslt = readAnnotationFile(viewport.getAlignment(), hidden,
             file, protocol);
-    if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns()))
+    if (rslt && (colSel.hasSelectedColumns() || hidden.hasHiddenColumns()))
     {
       viewport.setColumnSelection(colSel);
+      viewport.getAlignment().setHiddenColumns(hidden);
     }
 
     return rslt;
@@ -685,24 +716,44 @@ public class AnnotationFile
     return readAnnotationFile(al, null, file, sourceType);
   }
 
-  public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel,
+  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)
       {
@@ -710,11 +761,13 @@ public class AnnotationFile
         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 parseAnnotationFrom(al, colSel, in);
+        return parseAnnotationFrom(al, hidden, in);
       }
 
     } catch (Exception ex)
@@ -731,13 +784,8 @@ public class AnnotationFile
     return false;
   }
 
-  long nlinesread = 0;
-
-  String lastread = "";
 
-  private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE";
-
-  public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel,
+  public boolean parseAnnotationFrom(AlignmentI al, HiddenColumns hidden,
           BufferedReader in) throws Exception
   {
     nlinesread = 0;
@@ -929,12 +977,6 @@ public class AnnotationFile
           modified = true;
           continue;
         }
-        // else if (token.equalsIgnoreCase("VIEW_DEF"))
-        // {
-        // addOrSetView(al,st);
-        // modified = true;
-        // continue;
-        // }
         else if (token.equalsIgnoreCase("VIEW_SETREF"))
         {
           if (refSeq != null)
@@ -948,11 +990,11 @@ public class AnnotationFile
         {
           if (st.hasMoreTokens())
           {
-            if (colSel == null)
+            if (hidden == null)
             {
-              colSel = new ColumnSelection();
+              hidden = new HiddenColumns();
             }
-            parseHideCols(colSel, st.nextToken());
+            parseHideCols(hidden, st.nextToken());
           }
           modified = true;
           continue;
@@ -966,7 +1008,7 @@ public class AnnotationFile
           }
           if (sr != null)
           {
-            if (colSel == null)
+            if (hidden == null)
             {
               System.err
                       .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: "
@@ -975,13 +1017,64 @@ public class AnnotationFile
             else
             {
               // consider deferring this till after the file has been parsed ?
-              colSel.hideInsertionsFor(sr);
+              hidden.hideInsertionsFor(sr);
             }
           }
           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();
@@ -1181,7 +1274,101 @@ public class AnnotationFile
     return modified;
   }
 
-  private void parseHideCols(ColumnSelection colSel, String nextToken)
+
+  /**
+   * 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, ",");
     while (inval.hasMoreTokens())
@@ -1193,7 +1380,7 @@ public class AnnotationFile
         from = to = Integer.parseInt(range);
         if (from >= 0)
         {
-          colSel.hideColumns(from, to);
+          hidden.hideColumns(from, to);
         }
       }
       else
@@ -1209,7 +1396,7 @@ public class AnnotationFile
         }
         if (from > 0 && to >= from)
         {
-          colSel.hideColumns(from, to);
+          hidden.hideColumns(from, to);
         }
       }
     }
@@ -1610,8 +1797,7 @@ public class AnnotationFile
     if (sg != null)
     {
       String keyValue, key, value;
-      ColourSchemeI def = sg.cs;
-      sg.cs = null;
+      ColourSchemeI def = sg.getColourScheme();
       while (st.hasMoreTokens())
       {
         keyValue = st.nextToken();
@@ -1624,7 +1810,8 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("colour"))
         {
-          sg.cs = ColourSchemeProperty.getColourScheme(al, value);
+          sg.cs.setColourScheme(ColourSchemeProperty
+                  .getColourScheme(al, value));
         }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {
@@ -1677,9 +1864,8 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("idColour"))
         {
-          // consider warning if colour doesn't resolve to a real colour
-          def = new UserColourScheme(value);
-          sg.setIdColour(def.findColour());
+          Color idColour = ColorUtils.parseColourString(value);
+          sg.setIdColour(idColour == null ? Color.black : idColour);
         }
         else if (key.equalsIgnoreCase("hide"))
         {
@@ -1693,9 +1879,9 @@ public class AnnotationFile
         }
         sg.recalcConservation();
       }
-      if (sg.cs == null)
+      if (sg.getColourScheme() == null)
       {
-        sg.cs = def;
+        sg.setColourScheme(def);
       }
     }
   }
@@ -1789,7 +1975,7 @@ public class AnnotationFile
     return printAnnotations(viewport.isShowAnnotation() ? viewport
             .getAlignment().getAlignmentAnnotation() : null, viewport
             .getAlignment().getGroups(), viewport.getAlignment()
-            .getProperties(), viewport.getColumnSelection(),
+            .getProperties(), viewport.getAlignment().getHiddenColumns(),
             viewport.getAlignment(), null);
   }