fixed typos for modfinder chapter

jjgao · jjgao · commit ca00cb1c1856 · 2017-01-23T15:12:05.000-05:00
diff --git a/modfinder/add-protein-modification.md b/modfinder/add-protein-modification.md
@@ -1,4 +1,4 @@
-How to define a new protein modiifcation?
+How to define a new protein modifcation?
 ===
 
 The protmod module automatically loads [a list of protein modifications](supported-protein-modifications.md) into the protein modification registry. In case you have a protein modification that is not preloaded, it is possible to define it by yourself and add it into the registry.
@@ -84,7 +84,7 @@ ProteinModificationXmlReader.registerProteinModificationFromXml(fis);
 Navigation:
 [Home](../README.md)
 | [Book 6: The ModFinder Modules](README.md)
-| Chapter 4 - How to define a new protein modiifcation
+| Chapter 4 - How to define a new protein modifcation
 
 Prev: [Chapter 3 : How to identify protein modifications in a structure](identify-protein-modifications.md)
 
diff --git a/modfinder/identify-protein-modifications.md b/modfinder/identify-protein-modifications.md
@@ -7,7 +7,7 @@ How to identify protein modifications in a structure?
 Set<ModifiedCompound> identifyAllModfications(Structure struc) {
    ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
    parser.identify(struc);
-   Set`<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
+   Set<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
    return mcs;
 }
 ```
@@ -16,12 +16,12 @@ Set<ModifiedCompound> identifyAllModfications(Structure struc) {
 
 ```java
 List identifyPhosphosites(Structure struc) {
-    List<ResidueNumber> phosphosites = new ArrayList`();
+    List<ResidueNumber> phosphosites = new ArrayList<>();
     ProteinModificationIdentifier parser = new ProteinModificationIdentifier();
     parser.identify(struc, ProteinModificationRegistry.getByKeyword("phosphoprotein"));
-    Set mcs = parser.getIdentifiedModifiedCompound();
+    Set<ModifiedCompound> mcs = parser.getIdentifiedModifiedCompound();
     for (ModifiedCompound mc : mcs) {
-        Set` groups = mc.getGroups(true);
+        Set<StructureGroup> groups = mc.getGroups(true);
         for (StructureGroup group : groups) {
             phosphosites.add(group.getPDBResidueNumber());
         }
@@ -39,22 +39,22 @@ import org.biojava.nbio.structure.io.PDBFileReader;
 import org.biojava.nbio.protmod.structure.ProteinModificationIdentifier;
 
 public static void main(String[] args) {
-    try {`
+    try {
         PDBFileReader reader = new PDBFileReader();
         reader.setAutoFetch(true);
 
         // identify all modificaitons from PDB:1CAD and print them
         String pdbId = "1CAD";
         Structure struc = reader.getStructureById(pdbId);
-        Set mcs = identifyAllModfications(struc);
+        Set<ModifiedCompound> mcs = identifyAllModfications(struc);
         for (ModifiedCompound mc : mcs) {
             System.out.println(mc.toString());
         }
 
         // identify all phosphosites from PDB:3MVJ and print them
         pdbId = "3MVJ";
         struc = reader.getStructureById(pdbId);
-        List psites = identifyPhosphosites(struc);
+        List<ResidueNumber> psites = identifyPhosphosites(struc);
         for (ResidueNumber psite : psites) {
             System.out.println(psite.toString());
         }
@@ -72,4 +72,4 @@ Navigation:
 
 Prev: [Chapter 2 : How to get a list of supported protein modifications](supported-protein-modifications.md)
 
-Next: [Chapter 4 : How to define a new protein modiifcation](add-protein-modification.md)
+Next: [Chapter 4 : How to define a new protein modifcation](add-protein-modification.md)
diff --git a/modfinder/installation.md b/modfinder/installation.md
@@ -6,7 +6,7 @@ BioJava is open source and you can get the code from [Github](https://github.com
 
 BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html)  guide.
 
-As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:
+As of version 4, BioJava is available in maven central. This is all you would need to add BioJava dependencies to your project in the `pom.xml` file:
 
 ```xml
         <dependencies>
diff --git a/modfinder/supported-protein-modifications.md b/modfinder/supported-protein-modifications.md
@@ -1,7 +1,7 @@
 How to get a list of supported protein modifications?
 ===
 
-The protmod module contains [an XML file](https://github.com/biojava/biojava/blob/master/biojava-modfinder/src/main/resources/org/biojava/nbio/protmod/ptm_list.xml), defining a list of protein modifications, retrieved from [Protein Data Bank Chemical Component Dictrionary](http://www.wwpdb.org/ccd.html), [RESID](http://pir.georgetown.edu/resid/), and [PSI-MOD](http://www.psidev.info/MOD). It contains many common modifications such glycosylation, phosphorylation, acelytation, methylation, etc. Crosslinks are also included, such disulfide bonds and iso-peptide bonds.
+The protmod module contains [an XML file](https://github.com/biojava/biojava/blob/master/biojava-modfinder/src/main/resources/org/biojava/nbio/protmod/ptm_list.xml), defining a list of protein modifications, retrieved from [Protein Data Bank Chemical Component Dictionary](http://www.wwpdb.org/ccd.html), [RESID](http://pir.georgetown.edu/resid/), and [PSI-MOD](http://www.psidev.info/MOD). It contains many common modifications such glycosylation, phosphorylation, acelytation, methylation, etc. Crosslinks are also included, such disulfide bonds and iso-peptide bonds.
 
 The protmod maintains a registry of supported protein modifications. The list of protein modifications contained in the XML file will be automatically loaded. You can [define and register a new protein modification](add-protein-modification.md) if it has not been defined in the XML file. From the protein modification registry, a user can retrieve:
 - all protein modifications,
