JAL-2890 created tree job class that encapsulates all needed parameters

diff --git a/src/jalview/ext/cipres/TreeJob.java b/src/jalview/ext/cipres/TreeJob.java
new file mode 100644 (file)
index 0000000..1a0b550
--- /dev/null
+++ b/src/jalview/ext/cipres/TreeJob.java
@@ -0,0 +1,104 @@
+package jalview.ext.cipres;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.ngbw.directclient.CiApplication;
+import org.ngbw.directclient.CiClient;
+
+public class TreeJob
+{
+
+  private final CiClient cipresClient;
+
+  private final CiApplication app = CiApplication.getInstance();
+
+  private Map<String, Collection<String>> vParams = new HashMap<>();
+
+  private Map<String, String> inputParams = new HashMap<>();
+
+  private Map<String, String> metadata = new HashMap<>();
+
+  public TreeJob()
+  {
+    cipresClient = new CiClient(
+            app.getAppKey(), app.getUsername(), app.getPassword(),
+            app.getRestUrl()
+    );
+
+  }
+
+  public TreeJob(String alignmentFilePath)
+  {
+    cipresClient = new CiClient(
+            app.getAppKey(), app.getUsername(), app.getPassword(),
+            app.getRestUrl()
+    );
+    inputParams.put("infile_", alignmentFilePath);
+  }
+
+  /**
+   * Specifies a parameter about the input data for a CIPRES job with its value,
+   * for example the "infile_" parameter for the MSA file to calculate a tree
+   * from with file path as value.
+   * 
+   * @param parameter
+   * @param value
+   */
+  public void addInputParameter(String parameter, String value)
+  {
+    inputParams.put(parameter, value);
+
+  }
+
+  /**
+   * Adds a CIPRES tool parameter that specifies job behaviour, for example
+   * "runtime_" with the maximum runtime (in hours) as value.
+   * 
+   * @param parameter
+   * @param values
+   */
+  public void addToolParameters(String parameter, Collection<String> values)
+  {
+    vParams.put(parameter, values);
+  }
+
+  /**
+   * Adds a metadata tag to the job, for example "clientJobName" with the name
+   * that this job should be referred by as value. CIPRES highly recommends all
+   * jobs are given a clientJobId metadata header.
+   * 
+   * @param metadataHeader
+   * @param value
+   */
+  public void addMetadata(String metadataHeader, String value)
+  {
+    metadata.put(metadataHeader, value);
+  }
+
+  public void clearAllParameters()
+  {
+    vParams.clear();
+    inputParams.clear();
+    metadata.clear();
+  }
+
+  public void clearInputParameters()
+  {
+    inputParams.clear();
+  }
+
+  public void clearToolsParameters()
+  {
+    vParams.clear();
+  }
+
+  public void clearMetadata()
+  {
+    metadata.clear();
+  }
+
+
+
+}