From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 12 Jul 2016 20:55:14 +0000 (+0100)
Subject: FileFormat enum new types
X-Git-Tag: Release_2_10_3b1~412
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8dd4255a671e95df3fc6d6bc4d5d6b172f682c5d;p=jalview.git

FileFormat enum new types
---

diff --git a/src/jalview/io/AlignmentFileI.java b/src/jalview/io/AlignmentFileI.java
new file mode 100644
index 0000000..bee36f6
--- /dev/null
+++ b/src/jalview/io/AlignmentFileI.java
@@ -0,0 +1,40 @@
+package jalview.io;
+
+import jalview.api.AlignExportSettingI;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+public interface AlignmentFileI
+{
+
+  SequenceI[] getSeqsAsArray();
+
+  void addAnnotations(AlignmentI al);
+
+  void addGroups(AlignmentI al);
+
+  void setNewlineString(String newline);
+
+  void addJVSuffix(boolean jvsuffix);
+
+  void setExportSettings(AlignExportSettingI exportSettings);
+
+  void configureForView(AlignmentViewPanel viewpanel);
+
+  void setSeqs(SequenceI[] sequencesArray);
+
+  String print();
+
+  boolean hasWarningMessage();
+
+  String getWarningMessage();
+
+  String getInFile();
+
+  DataSourceType getDataSourceType();
+
+  FeatureSettingsModelI getFeatureColourScheme();
+
+}
diff --git a/src/jalview/io/DataSourceType.java b/src/jalview/io/DataSourceType.java
new file mode 100644
index 0000000..e2808e8
--- /dev/null
+++ b/src/jalview/io/DataSourceType.java
@@ -0,0 +1,6 @@
+package jalview.io;
+
+public enum DataSourceType
+{
+  FILE, URL, PASTE, CLASSLOADER;
+}
diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
new file mode 100644
index 0000000..893a8ac
--- /dev/null
+++ b/src/jalview/io/FileFormat.java
@@ -0,0 +1,481 @@
+package jalview.io;
+
+import jalview.ext.jmol.JmolParser;
+import jalview.structure.StructureImportSettings;
+
+import java.io.IOException;
+
+public enum FileFormat implements FileFormatI
+{
+  Fasta
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new FastaFile(inFile, sourceType);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new FastaFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new FastaFile();
+    }
+  },
+  Pfam
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new PfamFile(inFile, sourceType);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new PfamFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new PfamFile();
+    }
+  },
+  Stockholm
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new StockholmFile(inFile, sourceType);
+    }
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new StockholmFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new StockholmFile();
+    }
+
+  },
+  SimpleBlast
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new SimpleBlastFile(inFile, sourceType);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new SimpleBlastFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new SimpleBlastFile();
+    }
+  },
+
+  PIR
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new PIRFile(inFile, sourceType);
+    }
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new PIRFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new PIRFile();
+    }
+  },
+  BLC
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new BLCFile(inFile, sourceType);
+    }    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new BLCFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new BLCFile();
+    }
+
+  },
+  Html
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new HtmlFile(inFile, sourceType);
+    }    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new HtmlFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new HtmlFile();
+    }
+
+    @Override
+    public boolean isComplexAlignFile()
+    {
+      return true;
+    }
+
+  },
+  Rnaml
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new RnamlFile(inFile, sourceType);
+    }    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new RnamlFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new RnamlFile();
+    }
+
+  },
+  Json
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new JSONFile(inFile, sourceType);
+    }    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new JSONFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new JSONFile();
+    }
+
+    @Override
+    public boolean isComplexAlignFile()
+    {
+      return true;
+    }
+
+  },
+  Pileup
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new PileUpfile(inFile, sourceType);
+    }    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new PileUpfile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new PileUpfile();
+    }
+
+  },
+  MSF
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new MSFfile(inFile, sourceType);
+    }    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new MSFfile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new MSFfile();
+    }
+
+  },
+  Clustal
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new ClustalFile(inFile, sourceType);
+    }    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new ClustalFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new ClustalFile();
+    }
+
+  },
+  Phylip
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new PhylipFile(inFile, sourceType);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new PhylipFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new PhylipFile();
+    }
+
+  },
+  Jnet
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      JPredFile af = new JPredFile(inFile, sourceType);
+      af.removeNonSequences();
+      return af;
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      JPredFile af = new JPredFile(source);
+      af.removeNonSequences();
+      return af;
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return null; // todo is this called?
+    }
+
+  },
+  Features
+  {
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new FeaturesFile(true, inFile, sourceType);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new FeaturesFile(source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new FeaturesFile();
+    }
+  },
+  PDB
+  {
+
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      // TODO obtain config value from preference settings.
+      // Set value to 'true' to test PDB processing with Jmol: JAL-1213
+      boolean isParseWithJMOL = !StructureImportSettings
+              .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
+      if (isParseWithJMOL)
+      {
+        return new JmolParser(
+                StructureImportSettings.isVisibleChainAnnotation(),
+                StructureImportSettings.isPredictSecondaryStructure(),
+                StructureImportSettings.isExternalSecondaryStructure(),
+                inFile,
+                sourceType);
+      }
+      else
+      {
+        StructureImportSettings.setShowSeqFeatures(true);
+        return new MCview.PDBfile(
+                StructureImportSettings.isVisibleChainAnnotation(),
+                StructureImportSettings.isPredictSecondaryStructure(),
+                StructureImportSettings.isExternalSecondaryStructure(),
+                inFile,
+                sourceType);
+      }
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      boolean isParseWithJMOL = !StructureImportSettings
+              .getCurrentDefaultFormat().equalsIgnoreCase("PDB");
+      if (isParseWithJMOL)
+      {
+        return new JmolParser(
+                StructureImportSettings.isVisibleChainAnnotation(),
+                StructureImportSettings.isPredictSecondaryStructure(),
+                StructureImportSettings.isExternalSecondaryStructure(),
+                source);
+      }
+      else
+      {
+        StructureImportSettings.setShowSeqFeatures(true);
+        return new MCview.PDBfile(
+                StructureImportSettings.isVisibleChainAnnotation(),
+                StructureImportSettings.isPredictSecondaryStructure(),
+                StructureImportSettings.isExternalSecondaryStructure(),
+                source);
+      }
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new JmolParser(); // todo or null?
+    }
+
+  },
+  MMCif
+  {
+
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return new JmolParser(
+              StructureImportSettings.isVisibleChainAnnotation(),
+              StructureImportSettings.isPredictSecondaryStructure(),
+              StructureImportSettings.isExternalSecondaryStructure(),
+              inFile, sourceType);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return new JmolParser(
+              StructureImportSettings.isVisibleChainAnnotation(),
+              StructureImportSettings.isPredictSecondaryStructure(),
+              StructureImportSettings.isExternalSecondaryStructure(),
+              source);
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return new JmolParser(); // todo or null?
+    }
+  },
+  Jalview
+  {
+
+    @Override
+    public AlignmentFileI getAlignmentFile(String inFile,
+            DataSourceType sourceType) throws IOException
+    {
+      return null;
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile(FileParse source)
+            throws IOException
+    {
+      return null;
+    }
+
+    @Override
+    public AlignmentFileI getAlignmentFile()
+    {
+      return null;
+    }
+  };
+
+  @Override
+  public boolean isComplexAlignFile()
+  {
+    return false;
+  }
+
+  @Override
+  public String getShortDescription()
+  {
+    return toString();
+  }
+}
diff --git a/src/jalview/io/FileFormatException.java b/src/jalview/io/FileFormatException.java
new file mode 100644
index 0000000..c037cf2
--- /dev/null
+++ b/src/jalview/io/FileFormatException.java
@@ -0,0 +1,13 @@
+package jalview.io;
+
+import java.io.IOException;
+
+public class FileFormatException extends IOException
+{
+
+  public FileFormatException(String msg)
+  {
+    super(msg);
+  }
+
+}
diff --git a/src/jalview/io/FileFormatI.java b/src/jalview/io/FileFormatI.java
new file mode 100644
index 0000000..c9d56ae
--- /dev/null
+++ b/src/jalview/io/FileFormatI.java
@@ -0,0 +1,19 @@
+package jalview.io;
+
+import java.io.IOException;
+
+public interface FileFormatI
+{
+
+  AlignmentFileI getAlignmentFile(String inFile, DataSourceType sourceType)
+          throws IOException;
+
+  AlignmentFileI getAlignmentFile(FileParse source) throws IOException;
+
+  AlignmentFileI getAlignmentFile();
+
+  boolean isComplexAlignFile();
+
+  String getShortDescription();
+
+}