X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAppletFormatAdapter.java;h=8b7a4c2389ea3a30d47945dcefed3e6fc52fad45;hb=e57f77dc13f5a295cf49a403da05770a68a6e22b;hp=4c9324c35caa813c139086c63a07907fd0e67a7d;hpb=3e88ca066c0cc12f1f1f4c63e9cd49e19586b2bd;p=jalview.git

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 4c9324c..8b7a4c2 100755
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -20,22 +20,23 @@
  */
 package jalview.io;
 
-import jalview.api.AlignExportSettingI;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.List;
+import java.util.Locale;
+
+import jalview.api.AlignExportSettingsI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
-import jalview.datamodel.SeqDistanceContactMatrix;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.structure.StructureImportSettings;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.List;
+import jalview.util.Platform;
 
 /**
  * A low level class for alignment and feature IO with alignment formatting
@@ -65,7 +66,7 @@ public class AppletFormatAdapter
    */
   boolean serviceSecondaryStruct = false;
 
-  private AlignmentFileI alignFile = null;
+  private AlignmentFileReaderI alignFile = null;
 
   String inFile;
 
@@ -74,12 +75,22 @@ public class AppletFormatAdapter
    */
   protected String newline = System.getProperty("line.separator");
 
-  private AlignExportSettingI exportSettings;
+  private AlignExportSettingsI exportSettings;
+
+  private File selectedFile;
 
   public static String INVALID_CHARACTERS = "Contains invalid characters";
 
-  public static String SUPPORTED_FORMATS = "Formats currently supported are\n"
-          + prettyPrint(FileFormat.getReadableFormats());
+  /**
+   * Returns an error message with a list of supported readable file formats
+   * 
+   * @return
+   */
+  public static String getSupportedFormats()
+  {
+    return "Formats currently supported are\n"
+            + prettyPrint(FileFormats.getInstance().getReadableFormats());
+  }
 
   public AppletFormatAdapter()
   {
@@ -91,7 +102,7 @@ public class AppletFormatAdapter
   }
 
   public AppletFormatAdapter(AlignmentViewPanel alignPanel,
-          AlignExportSettingI settings)
+          AlignExportSettingsI settings)
   {
     viewpanel = alignPanel;
     exportSettings = settings;
@@ -140,7 +151,23 @@ public class AppletFormatAdapter
   public AlignmentI readFile(String file, DataSourceType sourceType,
           FileFormatI fileFormat) throws IOException
   {
-    this.inFile = file;
+    return readFile(null, file, sourceType, fileFormat);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat)
+          throws IOException
+  {
+    return readFile(selectedFile, file, sourceType, fileFormat, null);
+  }
+
+  public AlignmentI readFile(File selectedFile, String file,
+          DataSourceType sourceType, FileFormatI fileFormat,
+          StructureImportSettings.TFType tempfacType) throws IOException
+  {
+
+    this.selectedFile = selectedFile;
+    this.inFile = selectedFile != null ? selectedFile.getPath() : file;
     try
     {
       if (fileFormat.isStructureFile())
@@ -148,34 +175,47 @@ public class AppletFormatAdapter
         String structureParser = StructureImportSettings
                 .getDefaultPDBFileParser();
         boolean isParseWithJMOL = structureParser.equalsIgnoreCase(
-                        StructureImportSettings.StructureParser.JMOL_PARSER
-                                .toString());
+                StructureImportSettings.StructureParser.JMOL_PARSER
+                        .toString());
         StructureImportSettings.addSettings(annotFromStructure,
                 localSecondaryStruct, serviceSecondaryStruct);
+        if (tempfacType != null)
+        {
+          StructureImportSettings.setTemperatureFactorType(tempfacType);
+        }
         if (isParseWithJMOL)
         {
-          alignFile = new JmolParser(inFile, sourceType);
+          // needs a File option
+          alignFile = new JmolParser(
+                  selectedFile == null ? inFile : selectedFile, sourceType,
+                  StructureImportSettings.getTemperatureFactorType());
         }
         else
         {
-          // todo is MCview parsing obsolete yet?
+          // todo is mc_view parsing obsolete yet? JAL-2120
           StructureImportSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
+          alignFile = new mc_view.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, inFile,
                   sourceType);
         }
-        ((StructureFile) alignFile).setDbRefType(FileFormat.PDB
-                .equals(fileFormat) ? Type.PDB : Type.MMCIF);
+        ((StructureFile) alignFile).setDbRefType(
+                FileFormat.PDB.equals(fileFormat) ? Type.PDB : Type.MMCIF);
+      }
+      else if (selectedFile != null)
+      {
+        alignFile = fileFormat
+                .getReader(new FileParse(selectedFile, sourceType));
       }
       else
       {
-        alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+        // alignFile = fileFormat.getAlignmentFile(inFile, sourceType);
+        alignFile = fileFormat.getReader(new FileParse(inFile, sourceType));
       }
       return buildAlignmentFromFile();
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '"
+      jalview.bin.Console.errPrintln("Failed to read alignment using the '"
               + fileFormat + "' reader.\n" + e);
 
       if (e.getMessage() != null
@@ -209,7 +249,7 @@ public class AppletFormatAdapter
         throw new IOException(e.getMessage());
       }
     }
-    throw new FileFormatException(SUPPORTED_FORMATS);
+    throw new FileFormatException(getSupportedFormats());
   }
 
   /**
@@ -242,14 +282,14 @@ public class AppletFormatAdapter
         else
         {
           StructureImportSettings.setShowSeqFeatures(true);
-          alignFile = new MCview.PDBfile(annotFromStructure,
+          alignFile = new mc_view.PDBfile(annotFromStructure,
                   localSecondaryStruct, serviceSecondaryStruct, source);
         }
         ((StructureFile) alignFile).setDbRefType(Type.PDB);
       }
       else
       {
-        alignFile = format.getAlignmentFile(source);
+        alignFile = format.getReader(source);
       }
 
       return buildAlignmentFromFile();
@@ -257,8 +297,8 @@ public class AppletFormatAdapter
     } catch (Exception e)
     {
       e.printStackTrace();
-      System.err.println("Failed to read alignment using the '" + format
-              + "' reader.\n" + e);
+      jalview.bin.Console.errPrintln("Failed to read alignment using the '"
+              + format + "' reader.\n" + e);
 
       if (e.getMessage() != null
               && e.getMessage().startsWith(INVALID_CHARACTERS))
@@ -288,7 +328,7 @@ public class AppletFormatAdapter
       }
 
       // If we get to this stage, the format was not supported
-      throw new FileFormatException(SUPPORTED_FORMATS);
+      throw new FileFormatException(getSupportedFormats());
     }
   }
 
@@ -309,8 +349,6 @@ public class AppletFormatAdapter
 
     alignFile.addGroups(al);
 
-    al.addContactList(new SeqDistanceContactMatrix(al.getWidth()));
-
     return al;
   }
 
@@ -327,10 +365,10 @@ public class AppletFormatAdapter
           AlignmentViewPanel ap, boolean selectedOnly)
   {
 
-    AlignmentView selvew = ap.getAlignViewport().getAlignmentView(
-            selectedOnly, false);
-    AlignmentI aselview = selvew.getVisibleAlignment(ap.getAlignViewport()
-            .getGapCharacter());
+    AlignmentView selvew = ap.getAlignViewport()
+            .getAlignmentView(selectedOnly, false);
+    AlignmentI aselview = selvew
+            .getVisibleAlignment(ap.getAlignViewport().getGapCharacter());
     List<AlignmentAnnotation> ala = (ap.getAlignViewport()
             .getVisibleAlignmentAnnotation(selectedOnly));
     if (ala != null)
@@ -364,7 +402,7 @@ public class AppletFormatAdapter
   {
     try
     {
-      AlignmentFileI afile = format.getAlignmentFile(alignment);
+      AlignmentFileWriterI afile = format.getWriter(alignment);
 
       afile.setNewlineString(newline);
       afile.setExportSettings(exportSettings);
@@ -386,32 +424,60 @@ public class AppletFormatAdapter
       String afileresp = afile.print(seqs, jvsuffix);
       if (afile.hasWarningMessage())
       {
-        System.err.println("Warning raised when writing as " + format
-                + " : " + afile.getWarningMessage());
+        jalview.bin.Console.errPrintln("Warning raised when writing as "
+                + format + " : " + afile.getWarningMessage());
       }
       return afileresp;
     } catch (Exception e)
     {
-      System.err.println("Failed to write alignment as a '" + format
-              + "' file\n");
+      jalview.bin.Console.errPrintln("Failed to write alignment as a '"
+              + format.getName() + "' file\n");
       e.printStackTrace();
     }
 
     return null;
   }
 
-  public static DataSourceType checkProtocol(String file)
+  /**
+   * Determines the protocol (i.e DataSourceType.{FILE|PASTE|URL}) for the input
+   * data
+   * 
+   * BH 2018 allows File or String, and can return RELATIVE_URL
+   *
+   * @param dataObject
+   *          File or String
+   * @return the protocol for the input data
+   */
+  public static DataSourceType checkProtocol(Object dataObject)
   {
-    DataSourceType protocol = DataSourceType.FILE;
-    String ft = file.toLowerCase().trim();
+    if (dataObject instanceof File)
+    {
+      return DataSourceType.FILE;
+    }
+
+    String data = dataObject.toString();
+    DataSourceType protocol = DataSourceType.PASTE;
+    String ft = data.toLowerCase(Locale.ROOT).trim();
     if (ft.indexOf("http:") == 0 || ft.indexOf("https:") == 0
             || ft.indexOf("file:") == 0)
     {
       protocol = DataSourceType.URL;
     }
+    else if (Platform.isJS())
+    {
+      protocol = DataSourceType.RELATIVE_URL;
+    }
+    else if (new File(data).exists())
+    {
+      protocol = DataSourceType.FILE;
+    }
     return protocol;
   }
 
+  /**
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     int i = 0;
@@ -422,52 +488,53 @@ public class AppletFormatAdapter
       {
         try
         {
-          System.out.println("Reading file: " + f);
+          jalview.bin.Console.outPrintln("Reading file: " + f);
           AppletFormatAdapter afa = new AppletFormatAdapter();
           Runtime r = Runtime.getRuntime();
           System.gc();
           long memf = -r.totalMemory() + r.freeMemory();
           long t1 = -System.currentTimeMillis();
-          AlignmentI al = afa
-                  .readFile(args[i], DataSourceType.FILE,
-                          new IdentifyFile().identify(args[i],
-                                  DataSourceType.FILE));
+          AlignmentI al = afa.readFile(args[i], DataSourceType.FILE,
+                  new IdentifyFile().identify(args[i],
+                          DataSourceType.FILE));
           t1 += System.currentTimeMillis();
           System.gc();
           memf += r.totalMemory() - r.freeMemory();
           if (al != null)
           {
-            System.out.println("Alignment contains " + al.getHeight()
-                    + " sequences and " + al.getWidth() + " columns.");
+            jalview.bin.Console.outPrintln("Alignment contains "
+                    + al.getHeight() + " sequences and " + al.getWidth()
+                    + " columns.");
             try
             {
-              System.out.println(new AppletFormatAdapter().formatSequences(
-                      FileFormat.Fasta, al, true));
+              jalview.bin.Console.outPrintln(new AppletFormatAdapter()
+                      .formatSequences(FileFormat.Fasta, al, true));
             } catch (Exception e)
             {
-              System.err
-                      .println("Couln't format the alignment for output as a FASTA file.");
+              jalview.bin.Console.errPrintln(
+                      "Couln't format the alignment for output as a FASTA file.");
               e.printStackTrace(System.err);
             }
           }
           else
           {
-            System.out.println("Couldn't read alignment");
+            jalview.bin.Console.outPrintln("Couldn't read alignment");
           }
-          System.out.println("Read took " + (t1 / 1000.0) + " seconds.");
-          System.out
-                  .println("Difference between free memory now and before is "
+          jalview.bin.Console
+                  .outPrintln("Read took " + (t1 / 1000.0) + " seconds.");
+          jalview.bin.Console.outPrintln(
+                  "Difference between free memory now and before is "
                           + (memf / (1024.0 * 1024.0) * 1.0) + " MB");
         } catch (Exception e)
         {
-          System.err.println("Exception when dealing with " + i
+          jalview.bin.Console.errPrintln("Exception when dealing with " + i
                   + "'th argument: " + args[i] + "\n" + e);
         }
       }
       else
       {
-        System.err.println("Ignoring argument '" + args[i] + "' (" + i
-                + "'th)- not a readable file.");
+        jalview.bin.Console.errPrintln("Ignoring argument '" + args[i]
+                + "' (" + i + "'th)- not a readable file.");
       }
       i++;
     }
@@ -494,8 +561,9 @@ public class AppletFormatAdapter
     DataSourceType protocol = null;
     if (debug)
     {
-      System.out.println("resolving datasource started with:\n>>file\n"
-              + file + ">>endfile");
+      jalview.bin.Console
+              .outPrintln("resolving datasource started with:\n>>file\n"
+                      + file + ">>endfile");
     }
 
     // This might throw a security exception in certain browsers
@@ -512,7 +580,7 @@ public class AppletFormatAdapter
       }
       if (debug)
       {
-        System.err.println("Resource '" + file + "' was "
+        jalview.bin.Console.errPrintln("Resource '" + file + "' was "
                 + (rtn ? "" : "not") + " located by classloader.");
       }
       if (rtn)
@@ -540,8 +608,8 @@ public class AppletFormatAdapter
     {
       if (debug)
       {
-        System.out.println("Trying to get contents of resource as "
-                + protocol + ":");
+        jalview.bin.Console.outPrintln(
+                "Trying to get contents of resource as " + protocol + ":");
       }
       fp = new FileParse(file, protocol);
       if (!fp.isValid())
@@ -552,14 +620,15 @@ public class AppletFormatAdapter
       {
         if (debug)
         {
-          System.out.println("Successful.");
+          jalview.bin.Console.outPrintln("Successful.");
         }
       }
     } catch (Exception e)
     {
       if (debug)
       {
-        System.err.println("Exception when accessing content: " + e);
+        jalview.bin.Console
+                .errPrintln("Exception when accessing content: " + e);
       }
       fp = null;
     }
@@ -567,7 +636,7 @@ public class AppletFormatAdapter
     {
       if (debug)
       {
-        System.out.println("Accessing as paste.");
+        jalview.bin.Console.outPrintln("Accessing as paste.");
       }
       protocol = DataSourceType.PASTE;
       fp = null;
@@ -580,7 +649,8 @@ public class AppletFormatAdapter
         }
       } catch (Exception e)
       {
-        System.err.println("Failed to access content as paste!");
+        jalview.bin.Console
+                .errPrintln("Failed to access content as paste!");
         e.printStackTrace();
         fp = null;
       }
@@ -602,20 +672,22 @@ public class AppletFormatAdapter
         {
           if (debug)
           {
-            System.out.println("Format not identified. Inaccessible file.");
+            jalview.bin.Console.outPrintln(
+                    "Format not identified. Inaccessible file.");
           }
           return null;
         }
         if (debug)
         {
-          System.out.println("Format identified as " + idformat
+          jalview.bin.Console.outPrintln("Format identified as " + idformat
                   + "and expected as " + format);
         }
         if (idformat.equals(format))
         {
           if (debug)
           {
-            System.out.println("Protocol identified as " + protocol);
+            jalview.bin.Console
+                    .outPrintln("Protocol identified as " + protocol);
           }
           return protocol;
         }
@@ -633,7 +705,8 @@ public class AppletFormatAdapter
       {
         if (debug)
         {
-          System.err.println("File deemed not accessible via " + protocol);
+          jalview.bin.Console
+                  .errPrintln("File deemed not accessible via " + protocol);
           e.printStackTrace();
         }
       }
@@ -641,7 +714,7 @@ public class AppletFormatAdapter
     return null;
   }
 
-  public AlignmentFileI getAlignFile()
+  public AlignmentFileReaderI getAlignFile()
   {
     return alignFile;
   }