X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FFormat.java;h=a78123fd3f95ad29465e20bd5334369c52f9055d;hb=ff5f2b888385f85e9fd99a226c9da098a06016d8;hp=4c47f656a6b43c59121ebdd9d1ac8151ced28619;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/util/Format.java b/src/jalview/util/Format.java
index 4c47f65..a78123f 100755
--- a/src/jalview/util/Format.java
+++ b/src/jalview/util/Format.java
@@ -27,10 +27,16 @@
  */
 package jalview.util;
 
-import java.io.*;
 
 
-public class Format {
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Format
+{
     private int width;
     private int precision;
     private String pre;
@@ -42,7 +48,13 @@ public class Format {
     private boolean left_align;
     private char fmt; // one of cdeEfgGiosxXos
 
-    public Format(String s) {
+    /**
+     * Creates a new Format object.
+     *
+     * @param s DOCUMENT ME!
+     */
+    public Format(String s)
+    {
         width = 0;
         precision = -1;
         pre = "";
@@ -54,7 +66,6 @@ public class Format {
         left_align = false;
         fmt = ' ';
 
-        int state = 0;
         int length = s.length();
         int parse_state = 0;
 
@@ -62,41 +73,67 @@ public class Format {
         // 4 = format, 5 = end
         int i = 0;
 
-        while (parse_state == 0) {
-            if (i >= length) {
+        while (parse_state == 0)
+        {
+            if (i >= length)
+            {
                 parse_state = 5;
-            } else if (s.charAt(i) == '%') {
-                if (i < (length - 1)) {
-                    if (s.charAt(i + 1) == '%') {
+            }
+            else if (s.charAt(i) == '%')
+            {
+                if (i < (length - 1))
+                {
+                    if (s.charAt(i + 1) == '%')
+                    {
                         pre = pre + '%';
                         i++;
-                    } else {
+                    }
+                    else
+                    {
                         parse_state = 1;
                     }
-                } else {
+                }
+                else
+                {
                     throw new java.lang.IllegalArgumentException();
                 }
-            } else {
+            }
+            else
+            {
                 pre = pre + s.charAt(i);
             }
 
             i++;
         }
 
-        while (parse_state == 1) {
-            if (i >= length) {
+        while (parse_state == 1)
+        {
+            if (i >= length)
+            {
                 parse_state = 5;
-            } else if (s.charAt(i) == ' ') {
+            }
+            else if (s.charAt(i) == ' ')
+            {
                 show_space = true;
-            } else if (s.charAt(i) == '-') {
+            }
+            else if (s.charAt(i) == '-')
+            {
                 left_align = true;
-            } else if (s.charAt(i) == '+') {
+            }
+            else if (s.charAt(i) == '+')
+            {
                 show_plus = true;
-            } else if (s.charAt(i) == '0') {
+            }
+            else if (s.charAt(i) == '0')
+            {
                 leading_zeroes = true;
-            } else if (s.charAt(i) == '#') {
+            }
+            else if (s.charAt(i) == '#')
+            {
                 alternate = true;
-            } else {
+            }
+            else
+            {
                 parse_state = 2;
                 i--;
             }
@@ -104,43 +141,62 @@ public class Format {
             i++;
         }
 
-        while (parse_state == 2) {
-            if (i >= length) {
+        while (parse_state == 2)
+        {
+            if (i >= length)
+            {
                 parse_state = 5;
-            } else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9')) {
+            }
+            else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9'))
+            {
                 width = ((width * 10) + s.charAt(i)) - '0';
                 i++;
-            } else if (s.charAt(i) == '.') {
+            }
+            else if (s.charAt(i) == '.')
+            {
                 parse_state = 3;
                 precision = 0;
                 i++;
-            } else {
+            }
+            else
+            {
                 parse_state = 4;
             }
         }
 
-        while (parse_state == 3) {
-            if (i >= length) {
+        while (parse_state == 3)
+        {
+            if (i >= length)
+            {
                 parse_state = 5;
-            } else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9')) {
+            }
+            else if (('0' <= s.charAt(i)) && (s.charAt(i) <= '9'))
+            {
                 precision = ((precision * 10) + s.charAt(i)) - '0';
                 i++;
-            } else {
+            }
+            else
+            {
                 parse_state = 4;
             }
         }
 
-        if (parse_state == 4) {
-            if (i >= length) {
+        if (parse_state == 4)
+        {
+            if (i >= length)
+            {
                 parse_state = 5;
-            } else {
+            }
+            else
+            {
                 fmt = s.charAt(i);
             }
 
             i++;
         }
 
-        if (i < length) {
+        if (i < length)
+        {
             post = s.substring(i, length);
         }
     }
@@ -181,25 +237,29 @@ public class Format {
      * @exception IllegalArgumentException if bad format
      *
      */
-    public static String getHexString(java.awt.Color color) {
+    public static String getHexString(java.awt.Color color)
+    {
         String r;
         String g;
         String b;
         r = Integer.toHexString(color.getRed());
 
-        if (r.length() < 2) {
+        if (r.length() < 2)
+        {
             r = "0" + r;
         }
 
         g = Integer.toHexString(color.getGreen());
 
-        if (g.length() < 2) {
+        if (g.length() < 2)
+        {
             g = "0" + g;
         }
 
         b = Integer.toHexString(color.getBlue());
 
-        if (b.length() < 2) {
+        if (b.length() < 2)
+        {
             b = "0" + b;
         }
 
@@ -212,7 +272,8 @@ public class Format {
     * @param fmt the format string
     * @param x the double to print
     */
-    public static void print(java.io.PrintStream s, String fmt, double x) {
+    public static void print(java.io.PrintStream s, String fmt, double x)
+    {
         s.print(new Format(fmt).form(x));
     }
 
@@ -222,7 +283,8 @@ public class Format {
     * @param fmt the format string
     * @param x the long to print
     */
-    public static void print(java.io.PrintStream s, String fmt, long x) {
+    public static void print(java.io.PrintStream s, String fmt, long x)
+    {
         s.print(new Format(fmt).form(x));
     }
 
@@ -232,7 +294,8 @@ public class Format {
     * @param fmt the format string
     * @param x the character to
     */
-    public static void print(java.io.PrintStream s, String fmt, char x) {
+    public static void print(java.io.PrintStream s, String fmt, char x)
+    {
         s.print(new Format(fmt).form(x));
     }
 
@@ -241,7 +304,8 @@ public class Format {
     * @param s a PrintStream, fmt the format string
     * @param x a string that represents the digits to print
     */
-    public static void print(java.io.PrintStream s, String fmt, String x) {
+    public static void print(java.io.PrintStream s, String fmt, String x)
+    {
         s.print(new Format(fmt).form(x));
     }
 
@@ -250,7 +314,8 @@ public class Format {
     * @param s a string
     * @return the numeric value of the prefix of s representing a base 10 integer
     */
-    public static int atoi(String s) {
+    public static int atoi(String s)
+    {
         return (int) atol(s);
     }
 
@@ -259,25 +324,41 @@ public class Format {
     * @param s a string
     * @return the numeric value of the prefix of s representing a base 10 integer
     */
-    public static long atol(String s) {
+    public static long atol(String s)
+    {
         int i = 0;
 
         while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
             i++;
 
-        if ((i < s.length()) && (s.charAt(i) == '0')) {
+        if ((i < s.length()) && (s.charAt(i) == '0'))
+        {
             if (((i + 1) < s.length()) &&
-                    ((s.charAt(i + 1) == 'x') || (s.charAt(i + 1) == 'X'))) {
+                    ((s.charAt(i + 1) == 'x') || (s.charAt(i + 1) == 'X')))
+            {
                 return parseLong(s.substring(i + 2), 16);
-            } else {
+            }
+            else
+            {
                 return parseLong(s, 8);
             }
-        } else {
+        }
+        else
+        {
             return parseLong(s, 10);
         }
     }
 
-    private static long parseLong(String s, int base) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param base DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private static long parseLong(String s, int base)
+    {
         int i = 0;
         int sign = 1;
         long r = 0;
@@ -285,23 +366,34 @@ public class Format {
         while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
             i++;
 
-        if ((i < s.length()) && (s.charAt(i) == '-')) {
+        if ((i < s.length()) && (s.charAt(i) == '-'))
+        {
             sign = -1;
             i++;
-        } else if ((i < s.length()) && (s.charAt(i) == '+')) {
+        }
+        else if ((i < s.length()) && (s.charAt(i) == '+'))
+        {
             i++;
         }
 
-        while (i < s.length()) {
+        while (i < s.length())
+        {
             char ch = s.charAt(i);
 
-            if (('0' <= ch) && (ch < ('0' + base))) {
+            if (('0' <= ch) && (ch < ('0' + base)))
+            {
                 r = ((r * base) + ch) - '0';
-            } else if (('A' <= ch) && (ch < (('A' + base) - 10))) {
+            }
+            else if (('A' <= ch) && (ch < (('A' + base) - 10)))
+            {
                 r = ((r * base) + ch) - 'A' + 10;
-            } else if (('a' <= ch) && (ch < (('a' + base) - 10))) {
+            }
+            else if (('a' <= ch) && (ch < (('a' + base) - 10)))
+            {
                 r = ((r * base) + ch) - 'a' + 10;
-            } else {
+            }
+            else
+            {
                 return r * sign;
             }
 
@@ -315,45 +407,63 @@ public class Format {
     * Converts a string of digits to an double
     * @param s a string
     */
-    public static double atof(String s) {
+    public static double atof(String s)
+    {
         int i = 0;
         int sign = 1;
         double r = 0; // integer part
-        double f = 0; // fractional part
+        //double f = 0; // fractional part
         double p = 1; // exponent of fractional part
         int state = 0; // 0 = int part, 1 = frac part
 
         while ((i < s.length()) && Character.isWhitespace(s.charAt(i)))
             i++;
 
-        if ((i < s.length()) && (s.charAt(i) == '-')) {
+        if ((i < s.length()) && (s.charAt(i) == '-'))
+        {
             sign = -1;
             i++;
-        } else if ((i < s.length()) && (s.charAt(i) == '+')) {
+        }
+        else if ((i < s.length()) && (s.charAt(i) == '+'))
+        {
             i++;
         }
 
-        while (i < s.length()) {
+        while (i < s.length())
+        {
             char ch = s.charAt(i);
 
-            if (('0' <= ch) && (ch <= '9')) {
-                if (state == 0) {
+            if (('0' <= ch) && (ch <= '9'))
+            {
+                if (state == 0)
+                {
                     r = ((r * 10) + ch) - '0';
-                } else if (state == 1) {
+                }
+                else if (state == 1)
+                {
                     p = p / 10;
                     r = r + (p * (ch - '0'));
                 }
-            } else if (ch == '.') {
-                if (state == 0) {
+            }
+            else if (ch == '.')
+            {
+                if (state == 0)
+                {
                     state = 1;
-                } else {
+                }
+                else
+                {
                     return sign * r;
                 }
-            } else if ((ch == 'e') || (ch == 'E')) {
+            }
+            else if ((ch == 'e') || (ch == 'E'))
+            {
                 long e = (int) parseLong(s.substring(i + 1), 10);
 
                 return sign * r * Math.pow(10, e);
-            } else {
+            }
+            else
+            {
                 return sign * r;
             }
 
@@ -369,26 +479,33 @@ public class Format {
     * @return the formatted string
     * @exception IllegalArgumentException if bad argument
     */
-    public String form(double x) {
+    public String form(double x)
+    {
         String r;
 
-        if (precision < 0) {
+        if (precision < 0)
+        {
             precision = 6;
         }
 
         int s = 1;
 
-        if (x < 0) {
+        if (x < 0)
+        {
             x = -x;
             s = -1;
         }
 
-        if (fmt == 'f') {
+        if (fmt == 'f')
+        {
             r = fixed_format(x);
-        } else if ((fmt == 'e') || (fmt == 'E') || (fmt == 'g') ||
-                (fmt == 'G')) {
+        }
+        else if ((fmt == 'e') || (fmt == 'E') || (fmt == 'g') || (fmt == 'G'))
+        {
             r = exp_format(x);
-        } else {
+        }
+        else
+        {
             throw new java.lang.IllegalArgumentException();
         }
 
@@ -400,25 +517,38 @@ public class Format {
     * @param x the number to format
     * @return the formatted string
     */
-    public String form(long x) {
+    public String form(long x)
+    {
         String r;
         int s = 0;
 
-        if ((fmt == 'd') || (fmt == 'i')) {
-            if (x < 0) {
+        if ((fmt == 'd') || (fmt == 'i'))
+        {
+            if (x < 0)
+            {
                 r = ("" + x).substring(1);
                 s = -1;
-            } else {
+            }
+            else
+            {
                 r = "" + x;
                 s = 1;
             }
-        } else if (fmt == 'o') {
+        }
+        else if (fmt == 'o')
+        {
             r = convert(x, 3, 7, "01234567");
-        } else if (fmt == 'x') {
+        }
+        else if (fmt == 'x')
+        {
             r = convert(x, 4, 15, "0123456789abcdef");
-        } else if (fmt == 'X') {
+        }
+        else if (fmt == 'X')
+        {
             r = convert(x, 4, 15, "0123456789ABCDEF");
-        } else {
+        }
+        else
+        {
             throw new java.lang.IllegalArgumentException();
         }
 
@@ -430,8 +560,10 @@ public class Format {
     * @param x the value to format
     * @return the formatted string
     */
-    public String form(char c) {
-        if (fmt != 'c') {
+    public String form(char c)
+    {
+        if (fmt != 'c')
+        {
             throw new java.lang.IllegalArgumentException();
         }
 
@@ -445,12 +577,15 @@ public class Format {
     * @param x the value to format
     * @return the formatted string
     */
-    public String form(String s) {
-        if (fmt != 's') {
+    public String form(String s)
+    {
+        if (fmt != 's')
+        {
             throw new java.lang.IllegalArgumentException();
         }
 
-        if (precision >= 0) {
+        if (precision >= 0)
+        {
             s = s.substring(0, precision);
         }
 
@@ -460,7 +595,8 @@ public class Format {
     /**
     * a test stub for the format class
     */
-    public static void main(String[] a) {
+    public static void main(String[] a)
+    {
         double x = 1.23456789012;
         double y = 123;
         double z = 1.2345e30;
@@ -530,8 +666,18 @@ public class Format {
         Format.print(System.out, "|%6.0f|\n", 9.999);
     }
 
-    private static String repeat(char c, int n) {
-        if (n <= 0) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param c DOCUMENT ME!
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private static String repeat(char c, int n)
+    {
+        if (n <= 0)
+        {
             return "";
         }
 
@@ -543,14 +689,27 @@ public class Format {
         return s.toString();
     }
 
-    private static String convert(long x, int n, int m, String d) {
-        if (x == 0) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param x DOCUMENT ME!
+     * @param n DOCUMENT ME!
+     * @param m DOCUMENT ME!
+     * @param d DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private static String convert(long x, int n, int m, String d)
+    {
+        if (x == 0)
+        {
             return "0";
         }
 
         String r = "";
 
-        while (x != 0) {
+        while (x != 0)
+        {
             r = d.charAt((int) (x & m)) + r;
             x = x >>> n;
         }
@@ -558,66 +717,113 @@ public class Format {
         return r;
     }
 
-    private String pad(String r) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param r DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String pad(String r)
+    {
         String p = repeat(' ', width - r.length());
 
-        if (left_align) {
+        if (left_align)
+        {
             return pre + r + p + post;
-        } else {
+        }
+        else
+        {
             return pre + p + r + post;
         }
     }
 
-    private String sign(int s, String r) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param s DOCUMENT ME!
+     * @param r DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String sign(int s, String r)
+    {
         String p = "";
 
-        if (s < 0) {
+        if (s < 0)
+        {
             p = "-";
-        } else if (s > 0) {
-            if (show_plus) {
+        }
+        else if (s > 0)
+        {
+            if (show_plus)
+            {
                 p = "+";
-            } else if (show_space) {
+            }
+            else if (show_space)
+            {
                 p = " ";
             }
-        } else {
+        }
+        else
+        {
             if ((fmt == 'o') && alternate && (r.length() > 0) &&
-                    (r.charAt(0) != '0')) {
+                    (r.charAt(0) != '0'))
+            {
                 p = "0";
-            } else if ((fmt == 'x') && alternate) {
+            }
+            else if ((fmt == 'x') && alternate)
+            {
                 p = "0x";
-            } else if ((fmt == 'X') && alternate) {
+            }
+            else if ((fmt == 'X') && alternate)
+            {
                 p = "0X";
             }
         }
 
         int w = 0;
 
-        if (leading_zeroes) {
+        if (leading_zeroes)
+        {
             w = width;
-        } else if (((fmt == 'd') || (fmt == 'i') || (fmt == 'x') ||
-                (fmt == 'X') || (fmt == 'o')) && (precision > 0)) {
+        }
+        else if (((fmt == 'd') || (fmt == 'i') || (fmt == 'x') || (fmt == 'X') ||
+                (fmt == 'o')) && (precision > 0))
+        {
             w = precision;
         }
 
         return p + repeat('0', w - p.length() - r.length()) + r;
     }
 
-    private String fixed_format(double d) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param d DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String fixed_format(double d)
+    {
         boolean removeTrailing = ((fmt == 'G') || (fmt == 'g')) && !alternate;
 
         // remove trailing zeroes and decimal point
-        if (d > 0x7FFFFFFFFFFFFFFFL) {
+        if (d > 0x7FFFFFFFFFFFFFFFL)
+        {
             return exp_format(d);
         }
 
-        if (precision == 0) {
+        if (precision == 0)
+        {
             return (long) (d + 0.5) + (removeTrailing ? "" : ".");
         }
 
         long whole = (long) d;
         double fr = d - whole; // fractional part
 
-        if ((fr >= 1) || (fr < 0)) {
+        if ((fr >= 1) || (fr < 0))
+        {
             return exp_format(d);
         }
 
@@ -625,29 +831,33 @@ public class Format {
         String leading_zeroes = "";
 
         for (int i = 1; (i <= precision) && (factor <= 0x7FFFFFFFFFFFFFFFL);
-                i++) {
+                i++)
+        {
             factor *= 10;
             leading_zeroes = leading_zeroes + "0";
         }
 
         long l = (long) ((factor * fr) + 0.5);
 
-        if (l >= factor) {
+        if (l >= factor)
+        {
             l = 0;
             whole++;
         }
-         // CSH 10-25-97
 
+        // CSH 10-25-97
         String z = leading_zeroes + l;
         z = "." + z.substring(z.length() - precision, z.length());
 
-        if (removeTrailing) {
+        if (removeTrailing)
+        {
             int t = z.length() - 1;
 
             while ((t >= 0) && (z.charAt(t) == '0'))
                 t--;
 
-            if ((t >= 0) && (z.charAt(t) == '.')) {
+            if ((t >= 0) && (z.charAt(t) == '.'))
+            {
                 t--;
             }
 
@@ -657,45 +867,63 @@ public class Format {
         return whole + z;
     }
 
-    private String exp_format(double d) {
+    /**
+     * DOCUMENT ME!
+     *
+     * @param d DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    private String exp_format(double d)
+    {
         String f = "";
         int e = 0;
         double dd = d;
         double factor = 1;
 
-        if (d != 0) {
-            while (dd > 10) {
+        if (d != 0)
+        {
+            while (dd > 10)
+            {
                 e++;
                 factor /= 10;
                 dd = dd / 10;
             }
 
-            while (dd < 1) {
+            while (dd < 1)
+            {
                 e--;
                 factor *= 10;
                 dd = dd * 10;
             }
         }
 
-        if (((fmt == 'g') || (fmt == 'G')) && (e >= -4) && (e < precision)) {
+        if (((fmt == 'g') || (fmt == 'G')) && (e >= -4) && (e < precision))
+        {
             return fixed_format(d);
         }
 
         d = d * factor;
         f = f + fixed_format(d);
 
-        if ((fmt == 'e') || (fmt == 'g')) {
+        if ((fmt == 'e') || (fmt == 'g'))
+        {
             f = f + "e";
-        } else {
+        }
+        else
+        {
             f = f + "E";
         }
 
         String p = "000";
 
-        if (e >= 0) {
+        if (e >= 0)
+        {
             f = f + "+";
             p = p + e;
-        } else {
+        }
+        else
+        {
             f = f + "-";
             p = p + (-e);
         }