Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / src / jalview / bin / argparser / SubVals.java

diff --git a/src/jalview/bin/argparser/SubVals.java b/src/jalview/bin/argparser/SubVals.java
new file mode 100644 (file)
index 0000000..4d146d9
--- /dev/null
+++ b/src/jalview/bin/argparser/SubVals.java
@@ -0,0 +1,183 @@
+package jalview.bin.argparser;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import jalview.bin.Console;
+
+/**
+ * A helper class to parse a string of the possible forms "content"
+ * "[index]content", "[keyName=keyValue]content" and return the integer index,
+ * the strings keyName and keyValue, and the content after the square brackets
+ * (if present). Values not set `will be -1 or null.
+ */
+public class SubVals
+{
+  public static int NOTSET = -1;
+
+  private int index = NOTSET;
+
+  private Map<String, String> subValMap;
+
+  private static char SEPARATOR = ',';
+
+  private static char EQUALS = '=';
+
+  private String content = null;
+
+  protected SubVals(SubVals sv, String c)
+  {
+    this(sv, c, true);
+  }
+
+  protected SubVals(SubVals sv, String c, boolean merge)
+  {
+    SubVals subvals;
+    if (merge)
+    {
+      SubVals vsv = new SubVals(c);
+      if (sv != null && sv.getSubValMap() != null)
+      {
+        for (String key : sv.getSubValMap().keySet())
+        {
+          vsv.put(key, sv.get(key));
+        }
+      }
+      if (sv != null && sv.getIndex() > 0)
+      {
+        vsv.index = sv.getIndex();
+      }
+      subvals = vsv;
+    }
+    else
+    {
+      // replace
+      subvals = sv;
+    }
+    if (subvals == null)
+    {
+      this.subValMap = new HashMap<>();
+    }
+    else
+    {
+      this.subValMap = subvals == null ? new HashMap<>()
+              : subvals.getSubValMap();
+      this.index = subvals.getIndex();
+    }
+    this.content = c;
+  }
+
+  protected SubVals(String item)
+  {
+    if (subValMap == null)
+      subValMap = new HashMap<>();
+    this.parseVals(item);
+  }
+
+  public void parseVals(String item)
+  {
+    if (item == null)
+      return;
+    if (item.indexOf('[') == 0 && item.indexOf(']') > 1)
+    {
+      int openBracket = 0;
+      int closeBracket = item.indexOf(']');
+      String subvalsString = item.substring(openBracket + 1, closeBracket);
+      this.content = item.substring(closeBracket + 1);
+      boolean setIndex = false;
+      for (String subvalString : subvalsString
+              .split(Character.toString(SEPARATOR)))
+      {
+        int equals = subvalString.indexOf(EQUALS);
+        if (equals > -1)
+        {
+          this.put(subvalString.substring(0, equals),
+                  subvalString.substring(equals + 1));
+        }
+        else
+        {
+          try
+          {
+            this.index = Integer.parseInt(subvalString);
+            setIndex = true;
+          } catch (NumberFormatException e)
+          {
+            // store this non-numeric key as a "true" value
+            this.put(subvalString, "true");
+          }
+        }
+      }
+      if (!setIndex)
+        this.index = NOTSET;
+      else
+        Console.debug("SubVals from '" + subvalsString + "' has index "
+                + this.index + " set");
+    }
+    else
+    {
+      this.content = item;
+    }
+  }
+
+  protected void put(String key, String val)
+  {
+    subValMap.put(key, val);
+  }
+
+  public boolean notSet()
+  {
+    // notSet is true if content present but nonsensical
+    return index == NOTSET && (subValMap == null || subValMap.size() == 0);
+  }
+
+  public String getWithSubstitutions(ArgParser ap, String id, String key)
+  {
+    return ap.makeSubstitutions(subValMap.get(key), id);
+  }
+
+  public String get(String key)
+  {
+    return subValMap.get(key);
+  }
+
+  public boolean has(String key)
+  {
+    return subValMap.containsKey(key);
+  }
+
+  public int getIndex()
+  {
+    return index;
+  }
+
+  public String getContent()
+  {
+    return content;
+  }
+
+  protected Map<String, String> getSubValMap()
+  {
+    return subValMap;
+  }
+
+  public String toString()
+  {
+    if (subValMap == null && getIndex() == NOTSET)
+      return "";
+
+    StringBuilder sb = new StringBuilder();
+    List<String> entries = new ArrayList<>();
+    subValMap.entrySet().stream().forEachOrdered(
+            m -> entries.add(m.getValue().equals("true") ? m.getKey()
+                    : new StringBuilder().append(m.getKey()).append(EQUALS)
+                            .append(m.getValue()).toString()));
+    if (getIndex() != NOTSET)
+      entries.add(Integer.toString(getIndex()));
+    sb.append('[');
+    sb.append(String.join(Character.toString(SEPARATOR), entries));
+    sb.append(']');
+    return sb.toString();
+  }
+}
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