JAL-2344 separated AlignmentFileI into AlignmentFileReaderI,

AlignmentFileWriterI

diff --git a/examples/groovy/fileFormat.groovy b/examples/groovy/fileFormat.groovy
index 137fec6..c314a6c 100644 (file)
--- a/examples/groovy/fileFormat.groovy
+++ b/examples/groovy/fileFormat.groovy
@@ -3,7 +3,6 @@ import jalview.datamodel.SequenceI
 import jalview.datamodel.Sequence
 import jalview.io.FileFormatI
 import jalview.io.FileFormats
-import jalview.io.AlignmentFileI
 import jalview.io.FileParse
 import jalview.io.AlignFile
 

diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index d50fcef..c658734 100644 (file)
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -28,7 +28,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.io.AlignmentFileI;
+import jalview.io.AlignmentFileReaderI;
 import jalview.io.AnnotationFile;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
@@ -68,7 +68,7 @@ public class CutAndPasteTransfer extends Panel implements ActionListener,
 
   AlignFrame alignFrame;
 
-  AlignmentFileI source = null;
+  AlignmentFileReaderI source = null;
 
   public CutAndPasteTransfer(boolean forImport, AlignFrame alignFrame)
   {

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index a81c998..7a0b0af 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -30,7 +30,7 @@ import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
-import jalview.io.AlignmentFileI;
+import jalview.io.AlignmentFileReaderI;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
@@ -73,7 +73,7 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
 
   AlignViewportI viewport;
 
-  AlignmentFileI source = null;
+  AlignmentFileReaderI source = null;
 
   public CutAndPasteTransfer()
   {

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index cc5e816..7333075 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -40,7 +40,8 @@ import java.util.Vector;
  * @author $author$
  * @version $Revision$
  */
-public abstract class AlignFile extends FileParse implements AlignmentFileI
+public abstract class AlignFile extends FileParse implements
+        AlignmentFileReaderI, AlignmentFileWriterI
 {
   int noSeqs = 0;
 

diff --git a/src/jalview/io/AlignmentFileI.java b/src/jalview/io/AlignmentFileReaderI.java
similarity index 69%
rename from src/jalview/io/AlignmentFileI.java
rename to src/jalview/io/AlignmentFileReaderI.java
index 1a000a3..77a7643 100644 (file)
--- a/src/jalview/io/AlignmentFileI.java
+++ b/src/jalview/io/AlignmentFileReaderI.java
@@ -6,7 +6,7 @@ import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
 
-public interface AlignmentFileI
+public interface AlignmentFileReaderI
 {
 
   SequenceI[] getSeqsAsArray();
@@ -15,16 +15,8 @@ public interface AlignmentFileI
 
   void addGroups(AlignmentI al);
 
-  void setNewlineString(String newline);
-
-  void setExportSettings(AlignExportSettingI exportSettings);
-
-  void configureForView(AlignmentViewPanel viewpanel);
-
   void setSeqs(SequenceI[] sequencesArray);
 
-  String print(SequenceI[] seqs, boolean jvsuffix);
-
   boolean hasWarningMessage();
 
   String getWarningMessage();

diff --git a/src/jalview/io/AlignmentFileWriterI.java b/src/jalview/io/AlignmentFileWriterI.java
new file mode 100644 (file)
index 0000000..d8e2dd4
--- /dev/null
+++ b/src/jalview/io/AlignmentFileWriterI.java
@@ -0,0 +1,24 @@
+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 AlignmentFileWriterI
+{
+
+  void setNewlineString(String newline);
+
+  void setExportSettings(AlignExportSettingI exportSettings);
+
+  void configureForView(AlignmentViewPanel viewpanel);
+
+  String print(SequenceI[] seqs, boolean jvsuffix);
+
+  boolean hasWarningMessage();
+
+  String getWarningMessage();
+
+}

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 1bb7ba3..c5a80e3 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -64,7 +64,7 @@ public class AppletFormatAdapter
    */
   boolean serviceSecondaryStruct = false;
 
-  private AlignmentFileI alignFile = null;
+  private AlignmentFileReaderI alignFile = null;
 
   String inFile;
 
@@ -370,7 +370,7 @@ public class AppletFormatAdapter
   {
     try
     {
-      AlignmentFileI afile = format.getWriter(alignment);
+      AlignmentFileWriterI afile = format.getWriter(alignment);
 
       afile.setNewlineString(newline);
       afile.setExportSettings(exportSettings);
@@ -648,7 +648,7 @@ public class AppletFormatAdapter
     return null;
   }
 
-  public AlignmentFileI getAlignFile()
+  public AlignmentFileReaderI getAlignFile()
   {
     return alignFile;
   }

diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index 6d7042d..5a95a9e 100644 (file)
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -12,13 +12,14 @@ public enum FileFormat implements FileFormatI
   Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new FastaFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new FastaFile();
     }
@@ -26,13 +27,14 @@ public enum FileFormat implements FileFormatI
   Pfam("PFAM", "pfam", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new PfamFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PfamFile();
     }
@@ -40,13 +42,14 @@ public enum FileFormat implements FileFormatI
   Stockholm("Stockholm", "sto,stk", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new StockholmFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new StockholmFile(al);
     }
@@ -56,13 +59,14 @@ public enum FileFormat implements FileFormatI
   PIR("PIR", "pir", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new PIRFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PIRFile();
     }
@@ -70,13 +74,14 @@ public enum FileFormat implements FileFormatI
   BLC("BLC", "BLC", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new BLCFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new BLCFile();
     }
@@ -84,13 +89,14 @@ public enum FileFormat implements FileFormatI
   AMSA("AMSA", "amsa", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new AMSAFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new AMSAFile(al);
     }
@@ -98,13 +104,14 @@ public enum FileFormat implements FileFormatI
   Html("HTML", "html", true, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new HtmlFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new HtmlFile();
     }
@@ -119,13 +126,14 @@ public enum FileFormat implements FileFormatI
   Rnaml("RNAML", "xml,rnaml", true, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new RnamlFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new RnamlFile();
     }
@@ -134,13 +142,14 @@ public enum FileFormat implements FileFormatI
   Json("JSON", "json", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new JSONFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new JSONFile();
     }
@@ -155,13 +164,14 @@ public enum FileFormat implements FileFormatI
   Pileup("PileUp", "pileup", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new PileUpfile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PileUpfile();
     }
@@ -170,13 +180,14 @@ public enum FileFormat implements FileFormatI
   MSF("MSF", "msf", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new MSFfile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new MSFfile();
     }
@@ -185,13 +196,14 @@ public enum FileFormat implements FileFormatI
   Clustal("Clustal", "aln", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new ClustalFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new ClustalFile();
     }
@@ -199,13 +211,14 @@ public enum FileFormat implements FileFormatI
   Phylip("PHYLIP", "phy", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new PhylipFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new PhylipFile();
     }
@@ -213,7 +226,8 @@ public enum FileFormat implements FileFormatI
   Jnet("JnetFile", "", false, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       JPredFile af = new JPredFile(source);
       af.removeNonSequences();
@@ -221,7 +235,7 @@ public enum FileFormat implements FileFormatI
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return null; // todo is this called?
     }
@@ -230,13 +244,14 @@ public enum FileFormat implements FileFormatI
   Features("GFF or Jalview features", "gff2,gff3", true, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new FeaturesFile(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new FeaturesFile();
     }
@@ -244,7 +259,8 @@ public enum FileFormat implements FileFormatI
   PDB("PDB", "pdb,ent", true, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       boolean isParseWithJMOL = StructureImportSettings
               .getDefaultStructureFileFormat() != PDBEntry.Type.PDB;
@@ -264,7 +280,7 @@ public enum FileFormat implements FileFormatI
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new JmolParser(); // todo or null?
     }
@@ -278,13 +294,14 @@ public enum FileFormat implements FileFormatI
   MMCif("mmCIF", "cif", true, false)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return new JmolParser(source);
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return new JmolParser(); // todo or null?
     }
@@ -298,13 +315,14 @@ public enum FileFormat implements FileFormatI
   Jalview("Jalview", "jar,jvp", true, true)
   {
     @Override
-    public AlignmentFileI getReader(FileParse source) throws IOException
+    public AlignmentFileReaderI getReader(FileParse source)
+            throws IOException
     {
       return null;
     }
 
     @Override
-    public AlignmentFileI getWriter(AlignmentI al)
+    public AlignmentFileWriterI getWriter(AlignmentI al)
     {
       return null;
     }

diff --git a/src/jalview/io/FileFormatI.java b/src/jalview/io/FileFormatI.java
index 47b9103..e6f390d 100644 (file)
--- a/src/jalview/io/FileFormatI.java
+++ b/src/jalview/io/FileFormatI.java
@@ -6,9 +6,9 @@ import java.io.IOException;
 
 public interface FileFormatI
 {
-  AlignmentFileI getReader(FileParse source) throws IOException;
+  AlignmentFileReaderI getReader(FileParse source) throws IOException;
 
-  AlignmentFileI getWriter(AlignmentI al);
+  AlignmentFileWriterI getWriter(AlignmentI al);
 
   boolean isComplexAlignFile();
 

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index f137395..4f83ab1 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -53,7 +53,8 @@ public class FileLoader implements Runnable
 
   FileFormatI format;
 
-  AlignmentFileI source = null; // alternative specification of where data comes
+  AlignmentFileReaderI source = null; // alternative specification of where data
+                                      // comes
 
   // from
 
@@ -160,7 +161,7 @@ public class FileLoader implements Runnable
    * @param format
    * @return alignFrame constructed from file contents
    */
-  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source,
+  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
           FileFormatI format)
   {
     this.source = source;

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index ce584f2..d9dd79d 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -258,8 +258,8 @@ public class FormatAdapter extends AppletFormatAdapter
             selectedOnly);
   }
 
-  public AlignmentI readFromFile(AlignmentFileI source, FileFormatI format)
-          throws IOException
+  public AlignmentI readFromFile(AlignmentFileReaderI source,
+          FileFormatI format) throws IOException
   {
     FileParse fp = new FileParse(source.getInFile(),
             source.getDataSourceType());

diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java
index 72a1155..0556e76 100755 (executable)
--- a/src/jalview/io/IdentifyFile.java
+++ b/src/jalview/io/IdentifyFile.java
@@ -72,7 +72,7 @@ public class IdentifyFile
     // preserves original behaviour prior to version 2.3
   }
 
-  public FileFormatI identify(AlignmentFileI file, boolean closeSource)
+  public FileFormatI identify(AlignmentFileReaderI file, boolean closeSource)
           throws IOException
   {
     FileParse fp = new FileParse(file.getInFile(), file.getDataSourceType());