preliminary IO classes - read javadoc for purpose

diff --git a/src/jalview/io/ClansFile.java b/src/jalview/io/ClansFile.java
new file mode 100644 (file)
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--- /dev/null
+++ b/src/jalview/io/ClansFile.java
@@ -0,0 +1,10 @@
+package jalview.io;\r
+\r
+/**\r
+ * Read or write a CLANS style score matrix file. \r
+ */\r
+\r
+public class ClansFile extends FileParse\r
+{\r
+\r
+}\r

diff --git a/src/jalview/io/DBRefFile.java b/src/jalview/io/DBRefFile.java
new file mode 100644 (file)
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+++ b/src/jalview/io/DBRefFile.java
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+package jalview.io;\r
+\r
+import java.io.IOException;\r
+/**\r
+ * jalview flatfile for io of sequence ID mapping data\r
+ * DATABASE\t<nickname>\t<name>\t<version>... properties?jdbc, url, handler\r
+ * DBREF<seqID>\tDBID\taccno\t|seqstart,seqend,start,end...|\t|dbstart,dbend,...|\r
+ * \r
+ */\r
+public class DBRefFile extends AlignFile\r
+{\r
+\r
+  public void parse() throws IOException\r
+  {\r
+    // TODO Auto-generated method stub\r
+\r
+  }\r
+\r
+  public String print()\r
+  {\r
+    // TODO Auto-generated method stub\r
+    return null;\r
+  }\r
+\r
+}\r

diff --git a/src/jalview/io/MatrixFile.java b/src/jalview/io/MatrixFile.java
new file mode 100644 (file)
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+++ b/src/jalview/io/MatrixFile.java
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+package jalview.io;\r
+\r
+import java.io.IOException;\r
+\r
+/**\r
+ * IO for asymmetric matrix with arbitrary dimension\r
+ * with labels, as displayed by PCA viewer.\r
+ * Form is: tab separated entity defs\r
+ * header line\r
+ * TITLE\ttitle\r
+ * DESC\tdesc\r
+ * PROPERTY\t<id or empty for whole matrix>\tname\ttype\tvalue\r
+ * ROW\tRow i label (ID)/tPrinciple text/tprinciple description/t...\r
+ * COLUMN\t(similar, optional)..\r
+ * ..\r
+ * <float>\t<float>...(column-wise data for row i)\r
+ */\r
+ \r
+public class MatrixFile extends FileParse\r
+{ \r
+  \r
+}\r