From: jprocter <Jim Procter>
Date: Fri, 13 Jul 2007 15:37:21 +0000 (+0000)
Subject: preliminary IO classes - read javadoc for purpose
X-Git-Tag: Release_2_4~345
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=aa81abb776b73442af871aec2350b5721405f194;p=jalview.git

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
index 0000000..ee709e5
--- /dev/null
+++ b/src/jalview/io/ClansFile.java
@@ -0,0 +1,10 @@
+package jalview.io;
+
+/**
+ * Read or write a CLANS style score matrix file. 
+ */
+
+public class ClansFile extends FileParse
+{
+
+}
diff --git a/src/jalview/io/DBRefFile.java b/src/jalview/io/DBRefFile.java
new file mode 100644
index 0000000..f43a2a6
--- /dev/null
+++ b/src/jalview/io/DBRefFile.java
@@ -0,0 +1,25 @@
+package jalview.io;
+
+import java.io.IOException;
+/**
+ * jalview flatfile for io of sequence ID mapping data
+ * DATABASE\t<nickname>\t<name>\t<version>... properties?jdbc, url, handler
+ * DBREF<seqID>\tDBID\taccno\t|seqstart,seqend,start,end...|\t|dbstart,dbend,...|
+ * 
+ */
+public class DBRefFile extends AlignFile
+{
+
+  public void parse() throws IOException
+  {
+    // TODO Auto-generated method stub
+
+  }
+
+  public String print()
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
+}
diff --git a/src/jalview/io/MatrixFile.java b/src/jalview/io/MatrixFile.java
new file mode 100644
index 0000000..5b9e79f
--- /dev/null
+++ b/src/jalview/io/MatrixFile.java
@@ -0,0 +1,22 @@
+package jalview.io;
+
+import java.io.IOException;
+
+/**
+ * IO for asymmetric matrix with arbitrary dimension
+ * with labels, as displayed by PCA viewer.
+ * Form is: tab separated entity defs
+ * header line
+ * TITLE\ttitle
+ * DESC\tdesc
+ * PROPERTY\t<id or empty for whole matrix>\tname\ttype\tvalue
+ * ROW\tRow i label (ID)/tPrinciple text/tprinciple description/t...
+ * COLUMN\t(similar, optional)..
+ * ..
+ * <float>\t<float>...(column-wise data for row i)
+ */
+ 
+public class MatrixFile extends FileParse
+{ 
+  
+}