Merge pull request #10 from tomas-pluskal/minor_changes

Minor changes
mzmine · Apr 3, 2015 · cdd5ce3 · cdd5ce3
2 parents 86dc815 + 1f754b6
commit cdd5ce3
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Showing 5 changed files with 187 additions and 152 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,5 +1,6 @@
 .settings/
 target/
+conf/
 .DS_Store
 .project
-.classpath
+.classpath
diff --git a/...sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductSearchParameters.java b/...sf/mzmine/modules/peaklistmethods/identification/adductsearch/AdductSearchParameters.java
@@ -32,24 +32,28 @@ public class AdductSearchParameters extends SimpleParameterSet {
     public static final PeakListsParameter PEAK_LISTS = new PeakListsParameter();
 
     public static final RTToleranceParameter RT_TOLERANCE = new RTToleranceParameter(
-	    "RT tolerance",
-	    "Maximum allowed difference of retention time to set a relationship between peaks");
+            "RT tolerance",
+            "Maximum allowed difference of retention time to set a relationship between peaks");
 
     public static final AdductsParameter ADDUCTS = new AdductsParameter(
-	    "Adducts",
-	    "List of adducts, each one refers a specific distance in m/z axis between related peaks");
+            "Adducts",
+            "List of adducts, each one refers a specific distance in m/z axis between related peaks");
 
     public static final MZToleranceParameter MZ_TOLERANCE = new MZToleranceParameter(
-	    "m/z tolerance",
-	    "Tolerance value of the m/z difference between peaks");
+            "m/z tolerance",
+            "Tolerance value of the m/z difference between peaks");
 
+    /*
+     * Max value 10000% so even high-intensity adducts can be searched for.
+     */
     public static final PercentParameter MAX_ADDUCT_HEIGHT = new PercentParameter(
-	    "Max relative adduct peak height",
-	    "Maximum height of the recognized adduct peak, relative to the main peak");
+            "Max relative adduct peak height",
+            "Maximum height of the recognized adduct peak, relative to the main peak",
+            0.5, 0, 100);
 
     public AdductSearchParameters() {
 
-	super(new Parameter[] { PEAK_LISTS, RT_TOLERANCE, ADDUCTS,
-		MZ_TOLERANCE, MAX_ADDUCT_HEIGHT });
+        super(new Parameter[] { PEAK_LISTS, RT_TOLERANCE, ADDUCTS,
+                MZ_TOLERANCE, MAX_ADDUCT_HEIGHT });
     }
 }
diff --git a/.../mzmine/modules/peaklistmethods/identification/complexsearch/ComplexSearchParameters.java b/.../mzmine/modules/peaklistmethods/identification/complexsearch/ComplexSearchParameters.java
@@ -33,21 +33,25 @@ public class ComplexSearchParameters extends SimpleParameterSet {
     public static final PeakListsParameter peakLists = new PeakListsParameter();
 
     public static final ComboParameter<IonizationType> ionizationMethod = new ComboParameter<IonizationType>(
-	    "Ionization method",
-	    "Type of ion used to calculate the neutral mass",
-	    IonizationType.values());
+            "Ionization method",
+            "Type of ion used to calculate the neutral mass",
+            IonizationType.values());
 
     public static final RTToleranceParameter rtTolerance = new RTToleranceParameter();
 
     public static final MZToleranceParameter mzTolerance = new MZToleranceParameter();
 
+    /*
+     * Max value 10000% so even high-intensity complexes can be searched for.
+     */
     public static final PercentParameter maxComplexHeight = new PercentParameter(
-	    "Max complex peak height",
-	    "Maximum height of the recognized complex peak, relative to the highest of component peaks");
+            "Max complex peak height",
+            "Maximum height of the recognized complex peak, relative to the highest of component peaks",
+            0.5, 0, 100);
 
     public ComplexSearchParameters() {
-	super(new Parameter[] { peakLists, ionizationMethod, rtTolerance,
-		mzTolerance, maxComplexHeight });
+        super(new Parameter[] { peakLists, ionizationMethod, rtTolerance,
+                mzTolerance, maxComplexHeight });
     }
 
 }
diff --git a/...zmine/modules/peaklistmethods/identification/fragmentsearch/FragmentSearchParameters.java b/...zmine/modules/peaklistmethods/identification/fragmentsearch/FragmentSearchParameters.java
@@ -35,21 +35,25 @@ public class FragmentSearchParameters extends SimpleParameterSet {
     public static final RTToleranceParameter rtTolerance = new RTToleranceParameter();
 
     public static final MZToleranceParameter ms2mzTolerance = new MZToleranceParameter(
-	    "m/z tolerance of MS2 data",
-	    "Tolerance value of the m/z difference between peaks in MS/MS scans");
+            "m/z tolerance of MS2 data",
+            "Tolerance value of the m/z difference between peaks in MS/MS scans");
 
+    /*
+     * Max value 10000% so even high-intensity fragments can be searched for.
+     */
     public static final PercentParameter maxFragmentHeight = new PercentParameter(
-	    "Max fragment peak height",
-	    "Maximum height of the recognized fragment peak, relative to the main peak");
+            "Max fragment peak height",
+            "Maximum height of the recognized fragment peak, relative to the main peak",
+            0.5, 0, 100);
 
     public static final DoubleParameter minMS2peakHeight = new DoubleParameter(
-	    "Min MS2 peak height",
-	    "Minimum absolute intensity of the MS2 fragment peak", MZmineCore
-		    .getConfiguration().getIntensityFormat());
+            "Min MS2 peak height",
+            "Minimum absolute intensity of the MS2 fragment peak", MZmineCore
+                    .getConfiguration().getIntensityFormat());
 
     public FragmentSearchParameters() {
-	super(new Parameter[] { peakLists, rtTolerance, ms2mzTolerance,
-		maxFragmentHeight, minMS2peakHeight });
+        super(new Parameter[] { peakLists, rtTolerance, ms2mzTolerance,
+                maxFragmentHeight, minMS2peakHeight });
     }
 
 }